def design_matrix_event_related():
nidm_classes = {
"DesignMatrix_1stLevel": dict(
design_matrix_id='niiri:design_matrix_id',
label="Design Matrix",
location="file://./DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id",
regressors="",
design=q_graph.qname(NIDM_EVENT_RELATED_DESIGN),
hrf_basis="",
drift_model=""),
"ActivityUsedEntity": dict(
activity_id="niiri:model_parameter_estimation_id",
activity_type=q_graph.qname(NIDM_MODEL_PARAMETERS_ESTIMATION),
entity_id="niiri:design_matrix_id",
)
}
MIN_EX_DIR = os.path.join(os.path.dirname(
os.path.dirname(os.path.abspath(__file__))), 'test',
'minimal_examples', 'event_related_design')
ttl_file = os.path.join(MIN_EX_DIR, 'nidm.ttl')
example = ExampleFromTemplate(
nidm_classes, ttl_file, False,
remove_att=[NIDM_REGRESSOR_NAMES, NIDM_HAS_HRF_BASIS,
NIDM_HAS_DRIFT_MODEL])
example.create_example()
def explicit_mask():
nidm_classes = {
"MaskMap": dict(
mask_id="niiri:explicit_mask_id",
label="Mask Map",
location="",
filename="",
user_defined="true",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="",
used_by_act_id="niiri:model_parameter_estimation_id"
),
"ActivityUsedEntity": dict(
activity_id="niiri:model_parameter_estimation_id",
activity_type=q_graph.qname(NIDM_MODEL_PARAMETERS_ESTIMATION),
entity_id="niiri:explicit_mask_id",
)
}
MIN_EX_DIR = os.path.join(os.path.dirname(
os.path.dirname(os.path.abspath(__file__))), 'test',
'minimal_examples', 'explicit_mask')
ttl_file = os.path.join(MIN_EX_DIR, 'nidm.ttl')
example = ExampleFromTemplate(
nidm_classes, ttl_file, False, remove_att=[
NIDM_IN_COORDINATE_SPACE,
PROV.atLocation, NFO.fileName, CRYPTO.sha512, DC.description])
example.create_example()
def main():
nidm_classes = {
"HeightThreshold":
dict(
height_threshold_id="niiri:height_threshold_id",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
label="Height Threshold: p<0.05 (uncorrected)",
value="0.050000",
),
"ExtentThresholdStat":
dict(
extent_threshold_id="niiri:extent_threshold_id",
label="Extent Threshold: k>=0",
thresh_type=OBO_STATISTIC_QNAME,
cluster_size_vox="0",
),
"InferenceUsedThresh":
dict(
inference_id="niiri:inference_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
)
}
NIDM_FSL_DIR = os.path.join(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'fsl',
'example003')
ttl_file = os.path.join(NIDM_FSL_DIR, 'fsl_nidm.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def main():
nidm_classes = {
"DisplayMaskMap":
dict(display_map_id="niiri:display_map_id",
label="Display Mask Map",
location="file://./DisplayMask.nii.gz",
user_defined="true",
filename="DisplayMask.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a..."),
"CoordinateSpace-1":
dict(coordinate_space_id="niiri:coordinate_space_id_1",
label="Coordinate space 1",
voxel_to_world_mapping=
"[[-3, 0, 0, 78],[0, 3, 0, -112],[0, 0, 3, -70],[0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000051",
number_of_dim="3",
dimensions="[ 53, 63, 52 ]"),
"ActivityUsedEntity":
dict(
activity_id="niiri:display_map_id",
activity_type="nidm:NIDM_0000049",
entity_id="niiri:height_threshold_id",
)
}
NIDM_SPM_DIR = os.path.join(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'spm',
'example005')
ttl_file = os.path.join(NIDM_SPM_DIR, 'nidm.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def main():
nidm_classes = {
"HeightThreshold": dict(
height_threshold_id="niiri:height_threshold_id",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
label="Height Threshold: p<0.05 (uncorrected)",
value="0.050000",
),
"ExtentThresholdStat": dict(
extent_threshold_id="niiri:extent_threshold_id",
label="Extent Threshold: k>=0",
thresh_type=OBO_STATISTIC_QNAME,
cluster_size_vox="0",
),
"InferenceUsedThresh": dict(
inference_id="niiri:inference_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
)
}
NIDM_FSL_DIR = os.path.join(os.path.dirname(
os.path.dirname(os.path.abspath(__file__))), 'fsl', 'example003')
ttl_file = os.path.join(NIDM_FSL_DIR, 'fsl_nidm.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def main():
nidm_classes = {
"HeightThreshold": dict(
height_threshold_id="niiri:height_threshold_id",
thresh_type=OBO_P_VALUE_FWER_QNAME,
label="Height Threshold: p<0.05 (FWE)",
value="0.050000",
),
"ExtentThresholdStat": dict(
extent_threshold_id="niiri:extent_threshold_id",
label="Extent Threshold: k>=0",
thresh_type=OBO_STATISTIC_QNAME,
cluster_size_vox="0",
),
"InferenceUsedThresh": dict(
inference_id="niiri:inference_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
)
}
NIDM_FSL_DIR = os.path.join(os.path.dirname(
os.path.dirname(
os.path.abspath(__file__))), 'test', 'ground_truth',
'voxelwise_p050_fwe')
ttl_file = os.path.join(NIDM_FSL_DIR, 'nidm.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def main():
nidm_classes = {
"HeightThreshold_PFWE": dict(
height_threshold_id="niiri:height_threshold_id",
label="Height Threshold: p<0.05 (FWE)",
p_fwe="0.050000",
thresh_type="p-value FWE"
),
"FSL_ExtentThresholdNoType": dict(
extent_threshold_id="niiri:extent_threshold_id",
label="Extent Threshold: k>=0",
p_fwe="1.0"
),
"InferenceUsedThresh": dict(
inference_id="niiri:inference_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
)
}
NIDM_FSL_DIR = os.path.join(os.path.dirname(
os.path.dirname(os.path.abspath(__file__))), 'fsl', 'example002')
ttl_file = os.path.join(NIDM_FSL_DIR, 'fsl_nidm.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def explicit_mask():
nidm_classes = {
"MaskMap":
dict(mask_id="niiri:explicit_mask_id",
label="Mask Map",
location="",
filename="",
user_defined="true",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="",
used_by_act_id="niiri:model_parameter_estimation_id"),
"ActivityUsedEntity":
dict(
activity_id="niiri:model_parameter_estimation_id",
activity_type=q_graph.qname(NIDM_MODEL_PARAMETERS_ESTIMATION),
entity_id="niiri:explicit_mask_id",
)
}
MIN_EX_DIR = os.path.join(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'test',
'minimal_examples', 'explicit_mask')
ttl_file = os.path.join(MIN_EX_DIR, 'nidm.ttl')
example = ExampleFromTemplate(nidm_classes,
ttl_file,
False,
remove_att=[
NIDM_IN_COORDINATE_SPACE,
PROV.atLocation, NFO.fileName,
CRYPTO.sha512, DC.description
])
example.create_example()
def main():
nidm_classes = {
"DisplayMaskMap": dict(
display_map_id="niiri:display_map_id",
label="Display Mask Map",
location="file://./DisplayMask.nii.gz",
user_defined="true",
filename="DisplayMask.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a..."
),
"CoordinateSpace-1": dict(
coordinate_space_id="niiri:coordinate_space_id_1",
label="Coordinate space 1",
voxel_to_world_mapping="[[-3, 0, 0, 78],[0, 3, 0, -112],[0, 0, 3, -70],[0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000051",
number_of_dim="3",
dimensions="[ 53, 63, 52 ]"),
"ActivityUsedEntity": dict(
activity_id="niiri:display_map_id",
activity_type="nidm:NIDM_0000049",
entity_id="niiri:height_threshold_id",
)
}
NIDM_SPM_DIR = os.path.join(os.path.dirname(
os.path.dirname(os.path.abspath(__file__))), 'spm', 'example005')
ttl_file = os.path.join(NIDM_SPM_DIR, 'nidm.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def design_matrix_event_related():
nidm_classes = {
"DesignMatrix_1stLevel":
dict(design_matrix_id='niiri:design_matrix_id',
label="Design Matrix",
location="file://./DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id",
regressors="",
design=q_graph.qname(NIDM_EVENT_RELATED_DESIGN),
hrf_basis="",
drift_model=""),
"ActivityUsedEntity":
dict(
activity_id="niiri:model_parameter_estimation_id",
activity_type=q_graph.qname(NIDM_MODEL_PARAMETERS_ESTIMATION),
entity_id="niiri:design_matrix_id",
)
}
MIN_EX_DIR = os.path.join(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'test',
'minimal_examples', 'event_related_design')
ttl_file = os.path.join(MIN_EX_DIR, 'nidm.ttl')
example = ExampleFromTemplate(nidm_classes,
ttl_file,
False,
remove_att=[
NIDM_REGRESSOR_NAMES, NIDM_HAS_HRF_BASIS,
NIDM_HAS_DRIFT_MODEL
])
example.create_example()
def f_test():
nidm_classes = {
"ContrastExplainedMeanSquareMap":
dict(
id="niiri:contrast_explained_mean_square_map_id",
label="Contrast Explained Mean Square Map",
location="file://./ContrastExplainedMeanSquareMap_F001.nii.gz",
filename="ContrastExplainedMeanSquareMap_F001.nii.gz",
format="image/nifti",
coordinate_space_id="",
sha="",
contrast_est_id="niiri:contrast_estimation_id",
),
"EntityWasGeneratedByActivity":
dict(
activity_id="niiri:contrast_estimation_id",
activity_type=q_graph.qname(NIDM_CONTRAST_ESTIMATION),
entity_id="niiri:contrast_explained_mean_square_map_id",
)
}
MIN_EX_DIR = os.path.join(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'test',
'minimal_examples', 'f_test')
ttl_file = os.path.join(MIN_EX_DIR, 'nidm.ttl')
example = ExampleFromTemplate(
nidm_classes,
ttl_file,
False,
remove_att=[NIDM_IN_COORDINATE_SPACE, PROV.atLocation, CRYPTO.sha512])
example.create_example()
def main():
nidm_classes = {
"HeightThreshold":
dict(
height_threshold_id="niiri:height_threshold_id",
thresh_type=OBO_P_VALUE_FWER_QNAME,
label="Height Threshold: p<0.05 (FWE)",
value="0.050000",
),
"ExtentThresholdStat":
dict(
extent_threshold_id="niiri:extent_threshold_id",
label="Extent Threshold: k>=0",
thresh_type=OBO_STATISTIC_QNAME,
cluster_size_vox="0",
),
"InferenceUsedThresh":
dict(
inference_id="niiri:inference_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
)
}
NIDM_FSL_DIR = os.path.join(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'test',
'ground_truth', 'voxelwise_p050_fwe')
ttl_file = os.path.join(NIDM_FSL_DIR, 'nidm.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def f_test():
nidm_classes = {
"ContrastExplainedMeanSquareMap": dict(
id="niiri:contrast_explained_mean_square_map_id",
label="Contrast Explained Mean Square Map",
location="file://./ContrastExplainedMeanSquareMap_F001.nii.gz",
filename="ContrastExplainedMeanSquareMap_F001.nii.gz",
format="image/nifti",
coordinate_space_id="",
sha="",
contrast_est_id="niiri:contrast_estimation_id",
),
"EntityWasGeneratedByActivity": dict(
activity_id="niiri:contrast_estimation_id",
activity_type=q_graph.qname(NIDM_CONTRAST_ESTIMATION),
entity_id="niiri:contrast_explained_mean_square_map_id",
)
}
MIN_EX_DIR = os.path.join(os.path.dirname(
os.path.dirname(os.path.abspath(__file__))), 'test',
'minimal_examples', 'f_test')
ttl_file = os.path.join(MIN_EX_DIR, 'nidm.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False,
remove_att=[
NIDM_IN_COORDINATE_SPACE,
PROV.atLocation, CRYPTO.sha512])
example.create_example()
def main():
nidm_classes = {
"Inference": dict(
inference_id="niiri:inference_id_1",
label="Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id="niiri:statistic_map_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
display_mask_id="niiri:display_map_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"
),
"ConjunctionInference": dict(
conj_inference_id="niiri:conjunction_id_1",
label="Conjunction Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id_1="niiri:statistic_map_id_1",
stat_map_id_2="niiri:statistic_map_id_2",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
display_mask_id="niiri:display_map_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"
),
"SPM_KConjunctionInference": dict(
conj_inference_id="niiri:conjunction_id_2",
label="k-Conjunction Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id_1="niiri:statistic_map_id_1",
stat_map_id_2="niiri:statistic_map_id_2",
global_null_degree="1",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
display_mask_id="niiri:display_map_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"
),
}
NIDM_SPM_DIR = os.path.join(os.path.dirname(
os.path.dirname(os.path.abspath(__file__))), 'spm', "example004")
ttl_file = os.path.join(NIDM_SPM_DIR, 'spm_inference_activities.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def main():
nidm_classes = {
"Inference":
dict(inference_id="niiri:inference_id_1",
label="Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id="niiri:statistic_map_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
display_mask_id="niiri:display_map_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"),
"ConjunctionInference":
dict(conj_inference_id="niiri:conjunction_id_1",
label="Conjunction Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id_1="niiri:statistic_map_id_1",
stat_map_id_2="niiri:statistic_map_id_2",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
display_mask_id="niiri:display_map_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"),
"SPM_KConjunctionInference":
dict(conj_inference_id="niiri:conjunction_id_2",
label="k-Conjunction Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id_1="niiri:statistic_map_id_1",
stat_map_id_2="niiri:statistic_map_id_2",
global_null_degree="1",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
display_mask_id="niiri:display_map_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"),
}
NIDM_SPM_DIR = os.path.join(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'spm',
"example004")
ttl_file = os.path.join(NIDM_SPM_DIR, 'spm_inference_activities.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def main():
nidm_classes = {
"DesignMatrix":
dict(design_matrix_id='niiri:design_matrix_id',
label="Design Matrix",
location="DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id"),
"Image-DesignMatrix":
dict(image_id="niiri:design_matrix_png_id",
location="DesignMatrix.png",
filename="DesignMatrix.png",
format="image/png"),
"Data":
dict(data_id='niiri:data_id', label="Data", scaling="true",
target=100),
"ErrorModel":
dict(error_model_id="niiri:error_model_id",
noise_distribution="obo:STATO_0000227",
variance_homo="true",
variance_spatial="nidm:NIDM_0000073",
dependence="nidm:NIDM_0000048",
dependence_spatial="nidm:NIDM_0000073"),
"MaskMap-1":
dict( # Explicit mask used by Model Param. Est.
mask_id="niiri:mask_id_1",
label="Mask Map 1",
location="Mask_1.nii.gz",
filename="Mask_1.nii.gz",
user_defined="true",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
used_by_act_id="niiri:model_pe_id"),
"DerivedMap-MaskMap-1":
dict(derived_from_map_id="niiri:mask_id_1_der",
derived_map_type="nidm:NIDM_0000054",
filename="MaskMap_1_der.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a",
map_id="niiri:mask_id_1"),
"ModelParametersEstimation":
dict(model_pe_id="niiri:model_pe_id",
label="Model parameters estimation",
est_method=STATO_OLS_STR,
est_method_comment=STATO_OLS_LABEL,
design_matrix_id="niiri:design_matrix_id",
data_matrix_id="niiri:data_id",
error_model_id="niiri:error_model_id",
software_id="niiri:software_id"),
"ParameterEstimateMap_Location-1":
dict(beta_map_id="niiri:beta_map_id_1",
label="Beta Map 1",
location="ParameterEstimate_0001.nii.gz",
filename="ParameterEstimate_0001.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_pe_id"),
"DerivedMapWithHeader-PE1":
dict(derived_from_map_id="niiri:beta_map_id_1_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0001.img",
format="image/nifti",
derived_from_map_header_id="niiri:original_pe_map_header_id",
sha="e43b6e01b0463fe7d40782137867a",
format_header="image/nifti",
filename_header="beta_0001.hdr",
sha_header="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:beta_map_id_1"),
"ParameterEstimateMap_Location-2":
dict(beta_map_id="niiri:beta_map_id_2",
label="Beta Map 2",
location="ParameterEstimate_0002.nii",
filename="ParameterEstimate_0002.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_pe_id"),
"CoordinateSpace-1":
dict(coordinate_space_id="niiri:coordinate_space_id_1",
label="Coordinate space 1",
voxel_to_world_mapping=
"[[-3, 0, 0, 78],[0, 3, 0, -112],[0, 0, 3, -50],[0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000051",
number_of_dim="3",
dimensions="[ 53, 63, 46 ]"),
"ResidualMeanSquaresMap":
dict(residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
label="Residual Mean Squares Map",
location="ResidualMeanSquares.nii.gz",
filename="ResidualMeanSquares.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_pe_id"),
"MaskMap_Analysis":
dict( # Mask generated by Model Param. Est.
# (analysis mask)
mask_id="niiri:mask_id_2",
label="Mask Map 2",
location="Mask.nii.gz",
filename="Mask.nii.gz",
user_defined="false",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
generated_by_act_id="niiri:model_pe_id",
used_by_act_id="niiri:contrast_estimation_id"),
"DerivedMapWithHeader-Mask2":
dict(derived_from_map_id="niiri:mask_id_2_der",
derived_map_type="nidm:NIDM_0000054",
filename="mask.img",
format="image/nifti",
derived_from_map_header_id="niiri:original_mask_map_header_id",
sha="e43b6e01b0463fe7d40782137867a",
format_header="image/nifti",
filename_header="mask.hdr",
sha_header="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:mask_id_2"),
"ContrastWeights":
dict(contrast_id="niiri:contrast_id",
label="Contrast: Listening > Rest",
value="[ 1, 0, 0 ]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > rest"),
"ContrastEstimation":
dict(contrast_estimation_id="niiri:contrast_estimation_id",
label="Contrast estimation",
software_id="niiri:software_id",
mask_id="niiri:mask_id_2",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id",
param_est_map="niiri:beta_map_id_1"),
"ContrastEstUsedParamEst-Con1PE2":
dict(contrast_estimation_id="niiri:contrast_estimation_id",
param_est_map="niiri:beta_map_id_2"),
"ContrastMap":
dict(contrast_map_id="niiri:contrast_map_id",
label="Contrast Map: listening > rest",
location="Contrast.nii.gz",
format="image/nifti",
filename="Contrast.nii.gz",
contrast_name="listening > rest",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
contrast_est_id="niiri:contrast_estimation_id"),
"ContrastStandardErrorMap":
dict(contrast_standard_error_map_id=
"niiri:contrast_standard_error_map_id",
label="Contrast Standard Error Map",
location="ContrastStandardError.nii.gz",
format="image/nifti",
filename="ContrastStandardError.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
contrast_est_id="niiri:contrast_estimation_id"),
"StatisticMap_T":
dict(statistic_map_id="niiri:statistic_map_id",
label="Statistic Map: listening > rest",
location="TStatistic.nii.gz",
format="image/nifti",
filename="TStatistic.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > rest",
error_dof="72.9999999990787",
effect_dof="1",
sha="e43b6e01b0463fe7d40782137867a",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id"),
"DerivedMapWithHeader-StatMap":
dict(
derived_from_map_id="niiri:statistic_map_id_der",
derived_map_type="nidm:NIDM_0000076",
filename="spmT_0001.img",
format="image/nifti",
derived_from_map_header_id="niiri:statistic_original_map_header_id",
sha="e43b6e01b0463fe7d40782137867a",
format_header="image/nifti",
filename_header="spmT_0001.hdr",
sha_header="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:statistic_map_id"),
"HeightThreshold_equivThresh_equivThresh2":
dict(height_threshold_id="niiri:height_threshold_id",
thresh_type=OBO_P_VALUE_FWER_QNAME,
label="Height Threshold: p<0.05 (FWE)",
value="0.05",
equiv_thresh="niiri:height_threshold_id_2",
equiv_thresh2="niiri:height_threshold_id_3"),
"HeightThreshold-2":
dict(height_threshold_id="niiri:height_threshold_id_2",
thresh_type=OBO_STATISTIC_QNAME,
label="Height Threshold: p<5.23529984739211",
value="5.23529984739211"),
"HeightThreshold-3":
dict(
height_threshold_id="niiri:height_threshold_id_3",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
label="Height Threshold: p<7.62276079258051e-07 (uncorrected)",
value="7.62276079258051e-07",
),
"ExtentThresholdStat_equivThresh_equivThresh2_clusterSizeResels":
dict(extent_threshold_id="niiri:extent_threshold_id",
label="Extent Threshold: k>=0",
cluster_size_vox="0",
cluster_size_resels="0",
equiv_thresh="niiri:height_threshold_id_2",
equiv_thresh2="niiri:height_threshold_id_3"),
"ExtentThreshold-2":
dict(
extent_threshold_id="niiri:extent_threshold_id_2",
label="Extent Threshold",
thresh_type=OBO_P_VALUE_FWER_QNAME,
value="1",
),
"ExtentThreshold-3":
dict(
extent_threshold_id="niiri:extent_threshold_id_3",
label="Extent Threshold",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
value="1",
),
"DisplayMaskMap":
dict(display_map_id="niiri:display_map_id",
label="Display Mask Map",
location="DisplayMask.nii.gz",
format="image/nifti",
user_defined="true",
filename="DisplayMask.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_2",
sha="e43b6e01b0463fe7d40782137867a"),
"PeakDefinitionCriteria_MaxPeaks":
dict(peak_definition_criteria_id="niiri:peak_definition_criteria_id",
label="Peak Definition Criteria",
max_num_peaks="3",
min_dist_peaks="8.0"),
"ClusterDefinitionCriteria":
dict(cluster_definition_criteria_id=
"niiri:cluster_definition_criteria_id",
label="Cluster Connectivity Criterion: 18",
connectivity="nidm:NIDM_0000128"),
"MaskMap-2":
dict( # Explicit mask used by Inference
mask_id="niiri:mask_id_3",
label="Mask Map",
location="Mask_3.nii.gz",
filename="Mask_3.nii.gz",
user_defined="true",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_2",
sha="e43b6e01b0463fe7d40782137867a",
used_by_act_id="niiri:inference_id"),
"CoordinateSpace-2":
dict(coordinate_space_id="niiri:coordinate_space_id_2",
label="Coordinate space 2",
voxel_to_world_mapping=
"[[-3, 0, 0, 78],[0, 3, 0, -112],[0, 0, 3, -50],[0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000051",
number_of_dim="3",
dimensions="[ 53, 63, 46 ]"),
"Inference":
dict(inference_id="niiri:inference_id",
label="Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id="niiri:statistic_map_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
display_mask_id="niiri:display_map_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_2",
software_id="niiri:software_id"),
"ExcursionSetMap":
dict(
id="niiri:excursion_set_map_id",
label="Excursion Set Map",
location="ExcursionSet.nii.gz",
format="image/nifti",
filename="ExcursionSet.nii.gz",
cluster_label_map_id="niiri:cluster_label_map_id",
max_intensity_projection_id="niiri:maximum_intensity_projection_id",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
num_of_clusters="8",
p_value="8.95949980872501e-14",
inference_id="niiri:inference_id"),
"SupraThresholdCluster-1":
dict(cluster_id="niiri:supra_threshold_cluster_0001",
label="Supra-Threshold Cluster 0001",
cluster_size_in_voxels="530",
cluster_label_id="1",
cluster_size_in_resels="23.1209189500945",
p_value_unc="9.56276736481136e-52",
p_value_fwe="0",
p_value_fdr="7.65021389184909e-51",
excursion_set_id="niiri:excursion_set_map_id"),
"SupraThresholdCluster-2":
dict(cluster_id="niiri:supra_threshold_cluster_0002",
label="Supra-Threshold Cluster 0002",
cluster_size_in_voxels="445",
cluster_label_id="2",
cluster_size_in_resels="19.4128470430038",
p_value_unc="3.91543427861809e-46",
p_value_fwe="0",
p_value_fdr="1.56617371144723e-45",
excursion_set_id="niiri:excursion_set_map_id"),
"SupraThresholdCluster-3":
dict(cluster_id="niiri:supra_threshold_cluster_0003",
label="Supra-Threshold Cluster 0003",
cluster_size_in_voxels="38",
cluster_label_id="3",
cluster_size_in_resels="1.6577262643464",
p_value_unc="1.56592642027122e-09",
p_value_fwe="1.39237954499549e-10",
p_value_fdr="4.17580378738993e-09",
excursion_set_id="niiri:excursion_set_map_id"),
"Peak_ValueP-1":
dict(peak_id="niiri:peak_0001",
label="Peak 0001",
location="niiri:coordinate_0001",
value="13.9346199035645",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="6.3705194444993e-11",
cluster_id="niiri:supra_threshold_cluster_0001"),
"Coordinate-1":
dict(coordinate_id="niiri:coordinate_0001",
label="Coordinate: 0001",
coord="[ -60, -28, 13 ]"),
"Peak_ValueP-2":
dict(peak_id="niiri:peak_0002",
label="Peak 0002",
location="niiri:coordinate_0002",
value="11.3457498550415",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="3.12855975726156e-10",
cluster_id="niiri:supra_threshold_cluster_0001"),
"Coordinate-2":
dict(coordinate_id="niiri:coordinate_0002",
label="Coordinate: 0002",
coord="[ -66, -13, 4 ]"),
"Peak_ValueP-3":
dict(peak_id="niiri:peak_0003",
label="Peak 0003",
location="niiri:coordinate_0003",
value="9.82185649871826",
equiv_z="7.80404869241187",
p_uncorr="2.99760216648792e-15",
p_value_fwe="1.82057147135595e-10",
p_value_fdr="9.95383070867767e-08",
cluster_id="niiri:supra_threshold_cluster_0001"),
"Coordinate-3":
dict(coordinate_id="niiri:coordinate_0003",
label="Coordinate: 0003",
coord="[ -63, -7, -2 ]"),
"Peak_ValueP-4":
dict(peak_id="niiri:peak_0004",
label="Peak 0004",
location="niiri:coordinate_0004",
value="13.7208814620972",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="6.3705194444993e-11",
cluster_id="niiri:supra_threshold_cluster_0002"),
"Coordinate-4":
dict(coordinate_id="niiri:coordinate_0004",
label="Coordinate: 0004",
coord="[ 57, -22, 13 ]"),
"Peak_ValueP-5":
dict(peak_id="niiri:peak_0005",
label="Peak 0005",
location="niiri:coordinate_0005",
value="12.322901725769",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="6.3705194444993e-11",
cluster_id="niiri:supra_threshold_cluster_0002"),
"Coordinate-5":
dict(coordinate_id="niiri:coordinate_0005",
label="Coordinate: 0005",
coord="[ 66, -13, -2 ]"),
"Peak_ValueP-6":
dict(peak_id="niiri:peak_0006",
label="Peak 0006",
location="niiri:coordinate_0006",
value="9.62070846557617",
equiv_z="7.7026943536333",
p_uncorr="6.66133814775094e-15",
p_value_fwe="4.2237258135458e-10",
p_value_fdr="1.58195372181651e-07",
cluster_id="niiri:supra_threshold_cluster_0002"),
"Coordinate-6":
dict(coordinate_id="niiri:coordinate_0006",
label="Coordinate: 0006",
coord="[ 57, -40, 7 ]"),
"Peak_ValueP-7":
dict(peak_id="niiri:peak_0007",
label="Peak 0007",
location="niiri:coordinate_0007",
value="7.49709033966064",
equiv_z="6.43494304364426",
p_uncorr="6.17598194807556e-11",
p_value_fwe="4.05099727462943e-06",
p_value_fdr="0.000463130517859672",
cluster_id="niiri:supra_threshold_cluster_0003"),
"Coordinate-7":
dict(coordinate_id="niiri:coordinate_0007",
label="Coordinate: 0007",
coord="[ 36, -31, -14 ]"),
"SearchSpaceMaskMap":
dict(search_space_id="niiri:search_space_mask_id",
location="SearchSpaceMask.nii.gz",
filename="SearchSpaceMask.nii.gz",
label="Search Space Mask Map",
format="image/nifti",
user_defined="false",
coordinate_space_id="niiri:coordinate_space_id_2",
expected_num_voxels="0.553331387916112",
expected_num_clusters="0.0889172687960151",
height_critical_fwe05="5.23529984739211",
height_critical_fdr05="6.22537899017334",
smallest_size_fwe05="1",
smallest_size_fdr05="3",
search_vol_voxels="65593",
search_vol_units="1771011",
resel_size="22.9229643140043",
search_vol_resels="2552.68032521656",
search_vol_resels_geom=
"[3, 72.3216126440484, 850.716735116472, 2552.68032521656]",
noise_fwhm_in_voxels=
"[ 2.95881189165801, 2.96628446669584, 2.61180425626264 ]",
noise_fwhm_in_units=
"[ 8.87643567497404, 8.89885340008753, 7.83541276878791 ]",
random_field_station="false",
sha="e43b6e01b0463fe7d40782137867a",
inference_id="niiri:inference_id"),
"DerivedMapWithHeader":
dict(
derived_from_map_id="niiri:contrast_map_id_der",
derived_map_type="nidm:NIDM_0000002",
filename="con_0001.img",
format="image/nifti",
derived_from_map_header_id="niiri:original_contrast_map_header_id",
sha="e43b6e01b0463fe7d40782137867a",
format_header="image/nifti",
filename_header="con_0001.hdr",
sha_header="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:contrast_map_id"),
"DerivedMapWithHeader-2":
dict(derived_from_map_id="niiri:beta_map_id_2_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0002.img",
format="image/nifti",
derived_from_map_header_id="niiri:original_pe_map_header_2_id",
sha="e43b6e01b0463fe7d40782137867a",
format_header="image/nifti",
filename_header="beta_0002.hdr",
sha_header="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:beta_map_id_2"),
"DerivedMapWithHeader-3":
dict(
derived_from_map_id="niiri:statistic_map_id_der",
derived_map_type="nidm:NIDM_0000076",
filename="spmT_0001.img",
format="image/nifti",
derived_from_map_header_id="niiri:statistic_original_map_header_id",
sha="e43b6e01b0463fe7d40782137867a",
format_header="image/nifti",
filename_header="spmT_0001.hdr",
sha_header="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:statistic_map_id"),
"NIDMBundle":
dict(bundle_id="niiri:spm_results_id",
label="NIDM-Results",
object_model="nidm:NIDM_0000027",
version="1.1.0",
time="2014-05-19T10:30:00.000+01:00",
export_id="niiri:export_id"),
"SPM_ReselsPerVoxelMap":
dict(resels_per_voxel_map_id="niiri:resels_per_voxel_map_id",
label="Resels per Voxel Map",
location="ReselsPerVoxel.nii.gz",
filename="ReselsPerVoxel.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
model_pe_id="niiri:model_pe_id"),
"SPM_InferenceUsedRPVMap":
dict(inference_id="niiri:inference_id",
resels_per_voxel_map_id="niiri:resels_per_voxel_map_id"),
"DerivedMapWithHeader-4":
dict(derived_from_map_id="niiri:resels_per_voxel_map_id_der",
derived_map_type="nidm:NIDM_0000144",
filename="RPV.img",
format="image/nifti",
derived_from_map_header_id="niiri:original_rpv_map_header_id",
sha="e43b6e01b0463fe7d40782137867a",
format_header="image/nifti",
filename_header="RPV.hdr",
sha_header="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:resels_per_voxel_map_id"),
"ClusterLabelsMap":
dict(cluster_label_map_id="niiri:cluster_label_map_id",
location="ClusterLabels.nii.gz",
filename="ClusterLabels.nii.gz",
format="image/nifti"),
"SPM_Software":
dict(software_id="niiri:software_id",
software_type="nlx:nif-0000-00343",
label="SPM",
version="12b.5853"),
"Image":
dict(image_id="niiri:maximum_intensity_projection_id",
location="MaximumIntensityProjection.png",
filename="MaximumIntensityProjection.png",
format="image/png"),
"GrandMeanMap":
dict(grand_mean_map_id="niiri:grand_mean_map_id",
label="Grand Mean Map",
location="GrandMean.nii.gz",
filename="GrandMean.nii.gz",
format="image/nifti",
masked_median="115",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
model_pe_id="niiri:model_pe_id"),
"ExporterSoftware":
dict(software_id="niiri:exporter_id",
software_type="nidm:NIDM_0000168",
label="spm_results_nidm",
version="12b.5858"),
"Export":
dict(export_id="niiri:export_id",
label="NIDM-Results export",
exporter_id="niiri:exporter_id")
}
NIDM_SPM_DIR = os.path.join(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'spm')
ttl_file = os.path.join(NIDM_SPM_DIR, 'spm_results.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def main():
nidm_classes = {
"ImagingInstrument": dict(
id="niiri:mr_scanner_id",
label="MRI Scanner",
type=q_graph.qname(NLX_MRI_SCANNER),
),
"DesignMatrix_1stLevel": dict(
design_matrix_id='niiri:design_matrix_id',
label="Design Matrix",
location="DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id",
regressors="[\\\"Gen\\\", \\\"Gen*temporal_derivative\\\""
", \\\"Shad\\\", \\\"Shad*temporal_derivative\\\"]",
hrf_basis="fsl:FSL_0000001",
drift_model="niiri:drift_model_id"),
"FSL_DriftModel": dict(
id="niiri:drift_model_id",
label="FSL's Gaussian Running Line Drift Model",
cut_off="1908"
),
"Image-DesignMatrix": dict(
image_id="niiri:design_matrix_png_id",
location="DesignMatrix.png",
filename="DesignMatrix.png",
format="image/png"
),
"Person": dict(
id='niiri:subject_id',
label="Person"
),
"Data": dict(
data_id='niiri:data_id',
label="Data",
scaling="true",
target="10000",
scanner_id="niiri:mr_scanner_id",
sub_or_group_id="niiri:subject_id",
mr_protocol=q_graph.qname(NLX_FMRI_PROTOCOL)
),
"ErrorModel": dict(
error_model_id="niiri:error_model_id",
noise_distribution="obo:STATO_0000227",
variance_homo="true",
variance_spatial="nidm:NIDM_0000073",
dependence="obo:STATO_0000357",
dependence_spatial="nidm:NIDM_0000074"
),
"ModelParametersEstimation": dict(
model_pe_id="niiri:model_parameters_estimation_id",
label="Model Parameters Estimation",
est_method=STATO_GLS_STR,
est_method_comment=STATO_GLS_LABEL,
design_matrix_id="niiri:design_matrix_id",
data_matrix_id="niiri:data_id",
error_model_id="niiri:error_model_id",
software_id="niiri:software_id"
),
"ParameterEstimateMap-1": dict(
beta_map_id="niiri:beta_map_id_1",
label="Parameter estimate 1",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_parameters_estimation_id"),
"ParameterEstimateMap-2": dict(
beta_map_id="niiri:beta_map_id_2",
label="Parameter estimate 2",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_parameters_estimation_id"),
"ParameterEstimateMap-3": dict(
beta_map_id="niiri:beta_map_id_3",
label="Parameter estimate 3",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_parameters_estimation_id"),
"ParameterEstimateMap-4": dict(
beta_map_id="niiri:beta_map_id_4",
label="Parameter estimate 4",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_parameters_estimation_id"),
"CoordinateSpace": dict(
coordinate_space_id="niiri:coordinate_space_id_1",
label="Coordinate space",
voxel_to_world_mapping="[[ -3.5, 0, 0, 108.5], \
[ 0, 3.5, 0, -108.5], [ 0, 0, 3.5, -52.5], [ 0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3.5, 3.5, 3.5 ]",
coord_system="nidm:NIDM_0000077",
number_of_dim="3",
dimensions="[ 64, 64, 42 ]"),
"ResidualMeanSquaresMap": dict(
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
label="Residual Mean Squares Map",
location="ResidualMeanSquares.nii.gz",
filename="ResidualMeanSquares.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="1327a300eb1e20d42c67abb3c49a47b80ecabfebd13d0ba0aca0560e8bf43\
891f0e35a958c1afa84e041f62cf0038f58b4ab71f68b0b50d4153210aeed74f4ff",
param_est_id="niiri:model_parameters_estimation_id"),
"MaskMap_Analysis": dict( # Analysis mask
mask_id="niiri:mask_id_1",
label="Mask",
location="Mask.nii.gz",
filename="Mask.nii.gz",
user_defined="false",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="cc1a96a6111e5107eb08487e38e6d7f8164b9d1d3f1fc10948bdbcfaea642\
fe9bfae278c7fc372b65cac7232ea58fd8fb5914014e7b9a5d6200592b12b2a728b",
generated_by_act_id="niiri:model_parameters_estimation_id",
used_by_act_id="niiri:contrast_estimation_id_1"),
"ContrastWeights": dict(
contrast_id="niiri:contrast_id_1",
label="Contrast Weights: Generation",
value="[1, 0, 0, 0]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="Generation"
),
"ContrastEstimation": dict(
contrast_estimation_id="niiri:contrast_estimation_id_1",
label="Contrast estimation: Generation",
software_id="niiri:software_id",
mask_id="niiri:mask_id_1",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id_1",
param_est_map="niiri:beta_map_id_1"
),
"ContrastMap": dict(
contrast_map_id="niiri:contrast_map_id_1",
label="Contrast Map: Generation",
location="Contrast.nii.gz",
format="image/nifti",
filename="Contrast.nii.gz",
contrast_name="Generation",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="4c755c0ae6088f8001e0458f89e51fea0e2719b5dc747fed6f617ae12ad5c\
6a643e1afcb886bcabaaac7911f5e69086c1bd084af9f75dae75913d44a783151f6",
contrast_est_id="niiri:contrast_estimation_id_1"),
"ContrastStandardErrorMap": dict(
contrast_standard_error_map_id="niiri:contrast_standard_error_map\
_id_1",
label="Contrast Standard Error Map",
location="ContrastStandardError.nii.gz",
format="image/nifti",
filename="ContrastStandardError.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="8529f3ff9f10da8f332ced9d579990321475c1498b56d79ede560ba2eccf6\
d68718757dc7af78eb1e86617a41e6c9f55161f756d184e2b0fb06c3d419dc99856",
contrast_est_id="niiri:contrast_estimation_id_1"),
"DerivedMap-ContrastVariance": dict(
derived_from_map_id="niiri:d4de4b20b2d408cd8d825ac0edb6030a",
derived_map_type="nidm:NIDM_0000135",
filename="varcope1.nii.gz",
format="image/nifti",
sha="7d183bbacc0b99cd1db84174d32445457f532bca9f774fdcc53bc1d0faa5e\
7d250a1abf03864bd90b30f96f5a7516e0056104a729a565019b0f254a8a7bced1e",
map_id="niiri:contrast_standard_error_map_id_1"
),
"StatisticMap": dict(
statistic_map_id="niiri:statistic_map_id_1",
label="Statistic Map: Generation",
location="TStatistic.nii.gz",
format="image/nifti",
filename="TStatistic.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="Generation",
error_dof="102",
effect_dof="1",
sha="b6286d36e678c23622b5b0486f0efb5b274f9a5e2a3ee6aceb6a0338f7745\
fb8a4d8f72b8af22c4ffb40c860bfb65940c87b03a7336cdf1a665f9cb07a5c2527",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id_1"),
"StatisticMap-Z": dict(
statistic_map_id="niiri:z_statistic_map_id_1",
label="Z-Statistic Map: Generation",
location="ZStatistic.nii.gz",
format="image/nifti",
filename="ZStatistic.nii.gz",
statistic_type=STATO_ZSTATISTIC_STR,
stat_type_comment=STATO_ZSTATISTIC_LABEL,
contrast_name="Generation",
effect_dof="1",
error_dof="INF",
sha="3a68a4e5963766af86d22a871a4dbca9568a46441a567855b3a84dbd47ea0\
1acea11ed77b37ce85078a219adaa92264296a4548c1ba39b11ff028e8fefd95d03",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id_1"),
"HeightThreshold": dict(
height_threshold_id="niiri:height_threshold_id",
thresh_type=OBO_STATISTIC_QNAME,
label="Height Threshold: Z>2.3",
value="2.3",
),
"ExtentThreshold": dict(
extent_threshold_id="niiri:extent_threshold_id",
label="Extent Threshold: p<0.05 (FWE)",
thresh_type=OBO_P_VALUE_FWER_QNAME,
value="0.05",
),
"PeakDefinitionCriteria": dict(
peak_definition_criteria_id="niiri:peak_definition_criteria_id_1",
label="Peak Definition Criteria",
min_dist_peaks="0.0"
),
"ClusterDefinitionCriteria": dict(
cluster_definition_criteria_id="niiri:cluster_definition_criteria\
_id_1",
label="Cluster Connectivity Criterion: 26",
connectivity="nidm:NIDM_0000129"
),
"Inference": dict(
inference_id="niiri:inference_id_1",
label="Inference: Generation",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id="niiri:z_statistic_map_id_1",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
peak_def_id="niiri:peak_definition_criteria_id_1",
cluster_def_id="niiri:cluster_definition_criteria_id_1",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"
),
"FSL_ExcursionSetMap": dict(
id="niiri:excursion_set_map_id_1",
label="Excursion Set Map",
location="ExcursionSet.nii.gz",
format="image/nifti",
filename="ExcursionSet.nii.gz",
cluster_label_map_id="niiri:cluster_label_map_id",
png_id="niiri:excursion_set_png_id_1",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="c74e3c47e4308f27423a195c7c3e70b64b8fd362d612a2543da76bced67f6\
66949b70272033ab3d4b7d0bbbfe22b7da13d56d25521664be0c96454fd180ee4cc",
inference_id="niiri:inference_id_1"
),
"Image": dict(
image_id="niiri:excursion_set_png_id_1",
location="rendered_thresh_zstat1.png",
filename="rendered_thresh_zstat1.png",
format="image/png"
),
"FSL_SupraThresholdCluster-1": dict(
cluster_id="niiri:supra_threshold_cluster_0001",
label="Supra-Threshold Cluster 0001",
cluster_size_in_voxels="81",
cluster_label_id="1",
cluster_size_in_resels="23.1209189500945",
p_value_fwe="0.00894",
excursion_set_id="niiri:excursion_set_map_id_1"
),
"FSL_ClusterCenterOfGravity-1": dict(
center_of_gravity_id="niiri:center_of_gravity_1",
label="Center of gravity 1",
location="niiri:COG_coordinate_0001",
cluster_id="niiri:supra_threshold_cluster_0001"
),
"FSL_Coordinate-COG1": dict(
coordinate_id="niiri:COG_coordinate_0001",
label="Coordinate 0001",
coord="[ -5.8, 19.1, 38.5 ]",
coord_in_vox="[ 32.3, 39.2, 31.0 ]",
),
"FSL_SupraThresholdCluster-2": dict(
cluster_id="niiri:supra_threshold_cluster_0002",
label="Supra-Threshold Cluster 0002",
cluster_size_in_voxels="117",
cluster_label_id="2",
cluster_size_in_resels="19.4128470430038",
p_value_fwe="0.000621",
excursion_set_id="niiri:excursion_set_map_id_1"
),
"FSL_ClusterCenterOfGravity-2": dict(
center_of_gravity_id="niiri:center_of_gravity_2",
label="Center of gravity 2",
location="niiri:COG_coordinate_0002",
cluster_id="niiri:supra_threshold_cluster_0002"
),
"FSL_Coordinate-COG2": dict(
coordinate_id="niiri:COG_coordinate_0002",
label="Coordinate 0002",
coord="[ -56.9, -57.1, 9.86 ]",
coord_in_vox="[ 47.1, 19.2, 19.7 ]",
),
"FSL_SupraThresholdCluster-3": dict(
cluster_id="niiri:supra_threshold_cluster_0003 ",
label="Supra-Threshold Cluster 0003",
cluster_size_in_voxels="499",
cluster_label_id="3",
cluster_size_in_resels="19.4128470430038",
p_value_fwe="1.26e-12",
excursion_set_id="niiri:excursion_set_map_id_1"
),
"FSL_ClusterCenterOfGravity-3 ": dict(
center_of_gravity_id="niiri:center_of_gravity_3 ",
label="Center of gravity 3",
location="niiri:COG_coordinate_0003 ",
cluster_id="niiri:supra_threshold_cluster_0003 "
),
"FSL_Coordinate-COG3 ": dict(
coordinate_id="niiri:COG_coordinate_0003 ",
label="Coordinate 0003",
coord="[ -47.2, 17.3, 9.18 ]",
coord_in_vox="[ 43.4, 40.3, 23.9 ]",
),
"FSL_SupraThresholdCluster-4": dict(
cluster_id="niiri:supra_threshold_cluster_0004 ",
label="Supra-Threshold Cluster 0004",
cluster_size_in_voxels="1203",
cluster_label_id="4",
p_value_fwe="8.02e-24",
excursion_set_id="niiri:excursion_set_map_id_1"
),
"FSL_ClusterCenterOfGravity-4 ": dict(
center_of_gravity_id="niiri:center_of_gravity_4",
label="Center of gravity 4",
location="niiri:COG_coordinate_0004 ",
cluster_id="niiri:supra_threshold_cluster_0004 "
),
"FSL_Coordinate-COG4 ": dict(
coordinate_id="niiri:COG_coordinate_0004 ",
label="Coordinate 0004",
coord="[ -7.38, -72.5, -8.5 ]",
coord_in_vox="[ 34.0, 14.7, 14.0 ]",
),
"Peak-M4-1": dict(
peak_id="niiri:peak_0004_1",
label="Peak 0004_1",
p_uncorr="3.51932e-09",
location="niiri:coordinate_0004_1",
equiv_z="5.79",
cluster_id="niiri:supra_threshold_cluster_0004"
),
"FSL_Coordinate-4-1": dict(
coordinate_id="niiri:coordinate_0004_1",
label="Coordinate 0004_1",
coord="[ -33.7, -66.7, -14.7 ]",
coord_in_vox="[ 41, 17, 13 ]",
),
"Peak-4-2": dict(
peak_id="niiri:peak_0004_2",
label="Peak 0004_2",
p_uncorr="9.01048e-09",
location="niiri:coordinate_0004_2",
equiv_z="5.63",
cluster_id="niiri:supra_threshold_cluster_0004"
),
"FSL_Coordinate-4-2": dict(
coordinate_id="niiri:coordinate_0004_2",
label="Coordinate 0004_2",
coord="[ -38.0, -53.9, -21.9 ]",
coord_in_vox="[ 42, 21, 12 ]",
),
"Peak-4-3": dict(
peak_id="niiri:peak_0004_3",
label="Peak 0004_3",
p_uncorr="9.54787e-09",
location="niiri:coordinate_0004_3",
equiv_z="5.62",
cluster_id="niiri:supra_threshold_cluster_0004"
),
"FSL_Coordinate-4-3": dict(
coordinate_id="niiri:coordinate_0004_3",
label="Coordinate 0004_3",
coord="[ 16.1, -96.6, 5.82 ]",
coord_in_vox="[ 28, 7, 16 ]",
),
"Peak-4-4": dict(
peak_id="niiri:peak_0004_4",
label="Peak 0004_4",
p_uncorr="1.01163e-08",
location="niiri:coordinate_0004_4",
equiv_z="5.61",
cluster_id="niiri:supra_threshold_cluster_0004"
),
"FSL_Coordinate-4-4": dict(
coordinate_id="niiri:coordinate_0004_4",
label="Coordinate 0004_4",
coord="[ -48.1, -73.7, -9.24 ]",
coord_in_vox="[ 45, 15, 14 ]"
),
"Peak-4-5": dict(
peak_id="niiri:peak_0004_5",
label="Peak 0004_5",
p_uncorr="1.07176e-08",
location="niiri:coordinate_0004_5",
equiv_z="5.6",
cluster_id="niiri:supra_threshold_cluster_0004"
),
"FSL_Coordinate-4-5": dict(
coordinate_id="niiri:coordinate_0004_5",
label="Coordinate 0004_5",
coord="[ -25.5, -80.4, -15.3 ]",
coord_in_vox="[ 39, 13, 12 ]"
),
"Peak-4-6": dict(
peak_id="niiri:peak_0004_6",
label="Peak 0004_6",
p_uncorr="1.34887e-08",
location="niiri:coordinate_0004_6",
equiv_z="5.56",
cluster_id="niiri:supra_threshold_cluster_0004"
),
"FSL_Coordinate-4-6": dict(
coordinate_id="niiri:coordinate_0004_6",
label="Coordinate 0004_6",
coord="[ 0.791, -87.2, 3.23 ]",
coord_in_vox="[ 32, 10, 16 ]"
),
"Peak-M3-1": dict(
peak_id="niiri:peak_0003_1",
label="Peak 0003_1",
p_uncorr="1.01163e-08",
location="niiri:coordinate_0003_1",
equiv_z="5.61",
cluster_id="niiri:supra_threshold_cluster_0003"
),
"FSL_Coordinate-3-1": dict(
coordinate_id="niiri:coordinate_0003_1",
label="Coordinate 0003_1",
coord="[ -38.3, 20.7, 13.2 ]",
coord_in_vox="[ 41, 41, 25 ]"
),
"Peak-3-2": dict(
peak_id="niiri:peak_0003_2",
label="Peak 0003_2",
p_uncorr="1.52768e-07",
location="niiri:coordinate_0003_2",
equiv_z="5.12",
cluster_id="niiri:supra_threshold_cluster_0003"
),
"FSL_Coordinate-3-2": dict(
coordinate_id="niiri:coordinate_0003_2",
label="Coordinate 0003_2",
coord="[ -45.5, 17.8, -6.65 ]",
coord_in_vox="[ 43, 41, 20 ]"
),
"Peak-3-3": dict(
peak_id="niiri:peak_0003_3",
label="Peak 0003_3",
p_uncorr="1.82833e-06",
location="niiri:coordinate_0003_3",
equiv_z="4.63",
cluster_id="niiri:supra_threshold_cluster_0003"
),
"FSL_Coordinate-3-3": dict(
coordinate_id="niiri:coordinate_0003_3",
label="Coordinate 0003_3",
coord="[ -63.4, 3.78, 0.366 ]",
coord_in_vox="[ 48, 37, 21 ]"
),
"Peak-3-4": dict(
peak_id="niiri:peak_0003_4",
label="Peak 0003_4",
p_uncorr="9.77365e-06",
location="niiri:coordinate_0003_4",
equiv_z="4.27",
cluster_id="niiri:supra_threshold_cluster_0003"
),
"FSL_Coordinate-3-4": dict(
coordinate_id="niiri:coordinate_0003_4",
label="Coordinate 0003_4",
coord="[ -57.4, 31.8, -2.12 ]",
coord_in_vox="[ 46, 45, 22 ]"
),
"Peak-3-5": dict(
peak_id="niiri:peak_0003_5",
label="Peak 0003_5",
p_uncorr="1.22151e-05",
location="niiri:coordinate_0003_5",
equiv_z="4.22",
cluster_id="niiri:supra_threshold_cluster_0003"
),
"FSL_Coordinate-3-5": dict(
coordinate_id="niiri:coordinate_0003_5",
label="Coordinate 0003_5",
coord="[ -34.0, 8.84, 28.3 ]",
coord_in_vox="[ 40, 37, 28 ]"
),
"Peak-3-6": dict(
peak_id="niiri:peak_0003_6",
label="Peak 0003_6",
p_uncorr="1.89436e-05",
location="niiri:coordinate_0003_6",
equiv_z="4.12",
cluster_id="niiri:supra_threshold_cluster_0003"
),
"FSL_Coordinate-3-6": dict(
coordinate_id="niiri:coordinate_0003_6",
label="Coordinate 0003_6",
coord="[ -53.3, 23.3, 12.2 ]",
coord_in_vox="[ 45, 42, 25 ]"
),
"Peak-M2-1": dict(
peak_id="niiri:peak_0002_1",
label="Peak 0002_1",
p_uncorr="1.74205e-06",
location="niiri:coordinate_0002_1",
equiv_z="4.64",
cluster_id="niiri:supra_threshold_cluster_0002"
),
"FSL_Coordinate-2-1": dict(
coordinate_id="niiri:coordinate_0002_1",
label="Coordinate 0002_1",
coord="[ -56.2, -61.9, 4.03 ]",
coord_in_vox="[ 47, 18, 18 ]"
),
"Peak-2-2": dict(
peak_id="niiri:peak_0002_2",
label="Peak 0002_2",
p_uncorr="4.71165e-06",
location="niiri:coordinate_0002_2",
equiv_z="4.43",
cluster_id="niiri:supra_threshold_cluster_0002"
),
"FSL_Coordinate-2-2": dict(
coordinate_id="niiri:coordinate_0002_2",
label="Coordinate 0002_2",
coord="[ -56.7, -53.1, 18.2 ]",
coord_in_vox="[ 47, 20, 22 ]"
),
"Peak-M1-1": dict(
peak_id="niiri:peak_0001_1",
label="Peak 0001_1",
p_uncorr="2.01334e-06",
location="niiri:coordinate_0001_1",
equiv_z="4.61",
cluster_id="niiri:supra_threshold_cluster_0001"
),
"FSL_Coordinate-1-1": dict(
coordinate_id="niiri:coordinate_0001_1",
label="Coordinate 0001_1",
coord="[ -8.35, 15.1, 39.6 ]",
coord_in_vox="[ 33, 38, 31 ]"
),
"Peak-1-2": dict(
peak_id="niiri:peak_0001_2",
label="Peak 0001_2",
p_uncorr="0.000788846",
location="niiri:coordinate_0001_2",
equiv_z="3.16",
cluster_id="niiri:supra_threshold_cluster_0001"
),
"FSL_Coordinate-1-2": dict(
coordinate_id="niiri:coordinate_0001_2",
label="Coordinate 0001_2",
coord="[ -9.14, 30.5, 23.7 ]",
coord_in_vox="[ 33, 43, 28 ]"
),
"Peak-1-3": dict(
peak_id="niiri:peak_0001_3",
label="Peak 0001_3",
p_uncorr="0.00122277",
location="niiri:coordinate_0001_3",
equiv_z="3.03",
cluster_id="niiri:supra_threshold_cluster_0001"
),
"FSL_Coordinate-1-3": dict(
coordinate_id="niiri:coordinate_0001_3",
label="Coordinate 0001_3",
coord="[ -19.6, 17.4, 34.7 ]",
coord_in_vox="[ 36, 39, 30 ]"
),
"Peak-1-4": dict(
peak_id="niiri:peak_0001_4",
label="Peak 0001_4",
p_uncorr="0.00554262",
location="niiri:coordinate_0001_4",
equiv_z="2.54",
cluster_id="niiri:supra_threshold_cluster_0001"
),
"FSL_Coordinate-1-4": dict(
coordinate_id="niiri:coordinate_0001_4",
label="Coordinate 0001_4",
coord="[ -9.64, 40.1, 17.3 ]",
coord_in_vox="[ 33, 46, 27 ]"
),
"FSL_SearchSpaceMaskMap": dict(
search_space_id="niiri:search_space_mask_id",
location="SearchSpaceMask.nii.gz",
filename="SearchSpaceMask.nii.gz",
label="Search Space Mask Map",
user_defined="false",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
search_vol_voxels="45203",
search_vol_units="1.93808e+06",
search_vol_resels="3753.84",
resel_size="12.0418",
noise_roughness="0.384676",
random_field_station="true",
sha="cc1a96a6111e5107eb08487e38e6d7f8164b9d1d3f1fc10948bdbcfaea642\
fe9bfae278c7fc372b65cac7232ea58fd8fb5914014e7b9a5d6200592b12b2a728b",
inference_id="niiri:inference_id_1",
noise_fwhm_in_voxels="[2.38803, 2.43263, 2.07288]",
noise_fwhm_in_units="[8.35811, 8.5142, 7.2551]"
),
"NIDMBundle": dict(
bundle_id="niiri:fsl_results_id",
label="NIDM-Results",
object_model="nidm:NIDM_0000027",
version="1.1.0",
time="2014-05-19T10:30:00.000+01:00",
export_id="niiri:export_id"
),
"FSL_Software": dict(
software_id="niiri:software_id",
software_type="scr:SCR_002823",
label="FSL",
version="5.0.x",
feat_version="6.00"
),
"GrandMeanMap": dict(
grand_mean_map_id="niiri:grand_mean_map_id",
label="Grand Mean Map",
location="GrandMean.nii.gz",
filename="GrandMean.nii.gz",
format="image/nifti",
masked_median="9597.36",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="7a2703cea740e27a5170fb19e4a09b5e815e4b7e477bc75958404d675aa40\
8f53f747892a2ef4472f933cf5f12cd21cea99d5f5e551938081636fb6d4049473e",
model_pe_id="niiri:model_parameters_estimation_id"
),
"ExporterSoftware": dict(
software_id="niiri:exporter_id",
software_type="nidm:NIDM_0000167",
label="nidmfsl",
version="0.2.0"
),
"Export": dict(
export_id="niiri:export_id",
label="NIDM-Results export",
exporter_id="niiri:exporter_id"
)
}
NIDM_FSL_DIR = os.path.join(os.path.dirname(
os.path.dirname(os.path.abspath(__file__))), 'fsl', "example001")
ttl_file = os.path.join(NIDM_FSL_DIR, 'fsl_nidm.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def main():
nidm_classes = {
"ImagingInstrument": dict(
id="niiri:mr_scanner_id",
label="MRI Scanner",
type=q_graph.qname(NLX_MRI_SCANNER),
),
"DesignMatrix": dict(
design_matrix_id='niiri:design_matrix_id',
label="Design Matrix",
location="DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id"),
"Image-DesignMatrix": dict(
image_id="niiri:design_matrix_png_id",
location="DesignMatrix.png",
filename="DesignMatrix.png",
format="image/png"
),
"Group": dict(
id="niiri:group_id",
label="Group: Control",
name="Control",
numsubjects="23"
),
"Group-2": dict(
id="niiri:group2_id",
label="Group: Patient",
name="Patient",
numsubjects="21"
),
"Data_wasAttributedTo": dict(
data_id='niiri:data_id',
label="Data",
scaling="true",
target=100,
scanner_id="niiri:mr_scanner_id",
sub_or_group_id="niiri:group_id",
group2_id="niiri:group2_id",
mr_protocol=q_graph.qname(NLX_FMRI_PROTOCOL)
),
"ErrorModel": dict(
error_model_id="niiri:error_model_id",
noise_distribution="obo:STATO_0000227",
variance_homo="true",
variance_spatial="nidm:NIDM_0000073",
dependence="nidm:NIDM_0000048",
dependence_spatial="nidm:NIDM_0000073"
),
"ModelParametersEstimation": dict(
model_pe_id="niiri:model_pe_id",
label="Model parameters estimation",
est_method=STATO_OLS_STR,
est_method_comment=STATO_OLS_LABEL,
design_matrix_id="niiri:design_matrix_id",
data_matrix_id="niiri:data_id",
error_model_id="niiri:error_model_id",
software_id="niiri:software_id"
),
"ParameterEstimateMap_Location-1": dict(
beta_map_id="niiri:beta_map_id_1",
label="Beta Map 1",
location="ParameterEstimate_0001.nii.gz",
filename="ParameterEstimate_0001.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_pe_id"),
"DerivedMap-PE1": dict(
derived_from_map_id="niiri:beta_map_id_1_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0001.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a",
map_id="niiri:beta_map_id_1"
),
"ParameterEstimateMap_Location-2": dict(
beta_map_id="niiri:beta_map_id_2",
label="Beta Map 2",
location="ParameterEstimate_0002.nii.gz",
filename="ParameterEstimate_0002.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_pe_id"),
"DerivedMap-PE2": dict(
derived_from_map_id="niiri:beta_map_id_2_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0002.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a",
map_id="niiri:beta_map_id_2"
),
"ParameterEstimateMap_Location-3": dict(
beta_map_id="niiri:beta_map_id_3",
label="Beta Map 3",
location="ParameterEstimate_0003.nii.gz",
filename="ParameterEstimate_0003.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_pe_id"),
"DerivedMap-PE3": dict(
derived_from_map_id="niiri:beta_map_id_3_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0003.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a",
map_id="niiri:beta_map_id_3"
),
"CoordinateSpace-1": dict(
coordinate_space_id="niiri:coordinate_space_id_1",
label="Coordinate space 1",
voxel_to_world_mapping="[[-3, 0, 0, 78],[0, 3, 0, -112],[0, 0, 3, \
-50],[0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000051",
number_of_dim="3",
dimensions="[ 53, 63, 46 ]"),
"ResidualMeanSquaresMap": dict(
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
label="Residual Mean Squares Map",
location="ResidualMeanSquares.nii.gz",
filename="ResidualMeanSquares.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_pe_id"),
"MaskMap_Analysis": dict( # The analysis mask
mask_id="niiri:mask_id_1",
label="Mask",
location="Mask.nii.gz",
filename="Mask.nii.gz",
user_defined="false",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
generated_by_act_id="niiri:model_pe_id",
# fixme: also used by niiri:contrast_estimation_id_2
used_by_act_id="niiri:contrast_estimation_id"),
"ContrastWeights": dict(
contrast_id="niiri:contrast_id",
label="Contrast: listening > reading",
value="[1, -1, 0, 0]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > reading"
),
"ContrastWeights-2": dict(
contrast_id="niiri:contrast_id_2",
label="Contrast: motor",
value="[ 0, 0, 1 ]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="motor"
),
"ContrastEstimation": dict(
contrast_estimation_id="niiri:contrast_estimation_id",
label="Contrast estimation 1",
software_id="niiri:software_id",
mask_id="niiri:mask_id_1",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id",
param_est_map="niiri:beta_map_id_1"
),
"ContrastEstUsedParamEst-Con1PE2": dict(
contrast_estimation_id="niiri:contrast_estimation_id",
param_est_map="niiri:beta_map_id_2"
),
"ContrastEstimation-2": dict(
contrast_estimation_id="niiri:contrast_estimation_id_2",
label="Contrast estimation 2",
software_id="niiri:software_id",
mask_id="niiri:mask_id_1",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id_2",
param_est_map="niiri:beta_map_id_3"
),
"ContrastEstUsedParamEst-Con2PE3": dict(
contrast_estimation_id="niiri:contrast_estimation_id_2",
param_est_map="niiri:beta_map_id_3"
),
"ContrastMap": dict(
contrast_map_id="niiri:contrast_map_id",
label="Contrast Map: listening > reading",
location="Contrast_0001.nii.gz",
format="image/nifti",
filename="Contrast_0001.nii.gz",
contrast_name="listening > reading",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
contrast_est_id="niiri:contrast_estimation_id"),
"ContrastMap-2": dict(
contrast_map_id="niiri:contrast_map_id_2",
label="Contrast Map: motor",
location="Contrast_0002.nii.gz",
format="image/nifti",
filename="Contrast_0002.nii.gz",
contrast_name="motor",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
contrast_est_id="niiri:contrast_estimation_id_2"),
"DerivedMap-ContrastMap-2": dict(
derived_from_map_id="niiri:contrast_map_id_2_der",
derived_map_type="nidm:NIDM_0000002",
filename="con_0002.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a",
map_id="niiri:contrast_map_id_2"
),
"ContrastStandardErrorMap": dict(
contrast_standard_error_map_id="niiri:contrast_standard_error_map_\
id",
label="Contrast 1 Standard Error Map",
location="ContrastStandardError_0001.nii.gz",
format="image/nifti",
filename="ContrastStandardError_0001.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
contrast_est_id="niiri:contrast_estimation_id"),
"ContrastStandardErrorMap-2": dict(
contrast_standard_error_map_id="niiri:contrast_standard_error_map_\
id_2",
label="Contrast 2 Standard Error Map",
location="ContrastStandardError_0002.nii.gz",
format="image/nifti",
filename="ContrastStandardError_0002.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
contrast_est_id="niiri:contrast_estimation_id_2"),
"StatisticMap_T": dict(
statistic_map_id="niiri:statistic_map_id",
label="Statistic Map: listening > reading",
location="TStatistic_0001.nii.gz",
format="image/nifti",
filename="TStatistic_0001.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > reading",
error_dof="72.9999999990787",
effect_dof="1",
sha="e43b6e01b0463fe7d40782137867a",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id"),
"DerivedMap-StatMap": dict(
derived_from_map_id="niiri:statistic_map_id_der",
derived_map_type="nidm:NIDM_0000076",
filename="spmT_0001.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a",
map_id="niiri:statistic_map_id"
),
"StatisticMap_T-2": dict(
statistic_map_id="niiri:statistic_map_id_2",
label="Statistic Map: motor",
location="TStatistic_0002.nii.gz",
format="image/nifti",
filename="TStatistic_0002.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="motor",
error_dof="72.9999999990787",
effect_dof="1",
sha="e43b6e01b0463fe7d40782137867a",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id_2"),
"DerivedMap-StatMap-2": dict(
derived_from_map_id="niiri:statistic_map_id_2_der",
derived_map_type="nidm:NIDM_0000076",
filename="spmT_0002.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a",
map_id="niiri:statistic_map_id_2"
),
"HeightThreshold_equivThresh_equivThresh2": dict(
height_threshold_id="niiri:height_threshold_id",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
label="Height Threshold: p<7.62276079258051e-07 (unc)",
value="7.62276079258051e-07",
equiv_thresh="niiri:height_threshold_id_2",
equiv_thresh2="niiri:height_threshold_id_3"
),
"HeightThreshold-2": dict(
height_threshold_id="niiri:height_threshold_id_2",
thresh_type=OBO_STATISTIC_QNAME,
label="Height Threshold",
value="5.23529984739211"
),
"HeightThreshold-3": dict(
height_threshold_id="niiri:height_threshold_id_3",
thresh_type=OBO_P_VALUE_FWER_QNAME,
label="Height Threshold",
value="0.05",
),
"ExtentThresholdStat_equivThresh_equivThresh2_clusterSizeResels": dict(
extent_threshold_id="niiri:extent_threshold_id",
label="Extent Threshold: k>=10",
cluster_size_vox="10",
cluster_size_resels="3.3",
equiv_thresh="niiri:height_threshold_id_2",
equiv_thresh2="niiri:height_threshold_id_3"
),
"ExtentThreshold-2": dict(
extent_threshold_id="niiri:extent_threshold_id_2",
label="Extent Threshold",
thresh_type=OBO_P_VALUE_FWER_QNAME,
value="1",
),
"ExtentThreshold-3": dict(
extent_threshold_id="niiri:extent_threshold_id_3",
label="Extent Threshold",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
value="1",
),
"DisplayMaskMap": dict(
display_map_id="niiri:display_map_id",
label="Display Mask Map",
user_defined="true",
location="DisplayMask.nii.gz",
filename="DisplayMask.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a"
),
"PeakDefinitionCriteria_MaxPeaks": dict(
peak_definition_criteria_id="niiri:peak_definition_criteria_id",
label="Peak Definition Criteria",
max_num_peaks="3",
min_dist_peaks="8.0"
),
"ClusterDefinitionCriteria": dict(
cluster_definition_criteria_id="niiri:cluster_definition_criteria_\
id",
label="Cluster Connectivity Criterion: 18",
connectivity="nidm:NIDM_0000128"
),
"ConjunctionInference": dict(
conj_inference_id="niiri:inference_id",
label="Conjunction Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id_1="niiri:statistic_map_id",
stat_map_id_2="niiri:statistic_map_id_2",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
display_mask_id="niiri:display_map_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"
),
"SearchSpaceMaskMap": dict( # The "search space"
search_space_id="niiri:search_space_mask_id",
location="SearchSpaceMask.nii.gz",
filename="SearchSpaceMask.nii.gz",
label="Search Space Mask Map",
format="image/nifti",
user_defined="false",
coordinate_space_id="niiri:coordinate_space_id_1",
expected_num_voxels="4.02834655908613",
expected_num_clusters="0.0512932943875478",
height_critical_fwe05="4.85241745689539",
height_critical_fdr05="5.7639536857605",
smallest_size_fwe05="12",
smallest_size_fdr05="29",
search_vol_voxels="69306",
search_vol_units="1871262",
resel_size="132.907586178202",
search_vol_resels="467.07642343881",
search_vol_resels_geom="[7, 42.96312274763, 269.40914815306, \
467.07642343881]",
noise_fwhm_in_voxels="[ 5.41278985910694, 5.43638957240286, \
4.51666658877481 ]",
noise_fwhm_in_units="[ 16.2383695773208, 16.3091687172086, \
13.5499997663244 ]",
random_field_station="true",
sha="932fd9f0d55e9822748f4a9b35a0a7f0fe442f3e061e2eda48c2617a2938\
df50ea84deca8de0725641a0105b712a80a0c8931df9bdf3bef788b1041379d00875",
inference_id="niiri:inference_id"
),
"DerivedMap-Contrast": dict(
derived_from_map_id="niiri:contrast_map_id_der",
derived_map_type="nidm:NIDM_0000002",
filename="con_0001.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a",
map_id="niiri:contrast_map_id"
),
"NIDMBundle": dict(
bundle_id="niiri:spm_results_id",
label="NIDM-Results",
object_model="nidm:NIDM_0000027",
version="1.1.0",
time="2014-05-19T10:30:00.000+01:00",
export_id="niiri:export_id"
),
"SPM_ReselsPerVoxelMap": dict(
resels_per_voxel_map_id="niiri:resels_per_voxel_map_id",
label="Resels per Voxel Map",
location="ReselsPerVoxel.nii.gz",
filename="ReselsPerVoxel.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
model_pe_id="niiri:model_pe_id"
),
"SPM_InferenceUsedRPVMap": dict(
inference_id="niiri:inference_id",
resels_per_voxel_map_id="niiri:resels_per_voxel_map_id"
),
"DerivedMap-RPV": dict(
derived_from_map_id="niiri:resels_per_voxel_map_id_der",
derived_map_type="nidm:NIDM_0000144",
filename="RPV.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a",
map_id="niiri:resels_per_voxel_map_id"
),
"SPM_Software": dict(
software_id="niiri:software_id",
software_type="scr:SCR_007037",
label="SPM",
version="12b.5853"
),
"GrandMeanMap": dict(
grand_mean_map_id="niiri:grand_mean_map_id",
label="Grand Mean Map",
location="GrandMean.nii.gz",
filename="GrandMean.nii.gz",
format="image/nifti",
masked_median="115",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
model_pe_id="niiri:model_pe_id"
),
"ExporterSoftware": dict(
software_id="niiri:exporter_id",
software_type="nidm:NIDM_0000168",
label="spm_results_nidm",
version="12b.5858"
),
"Export": dict(
export_id="niiri:export_id",
label="NIDM-Results export",
exporter_id="niiri:exporter_id"
),
"ExcursionSetMap": dict(
id="niiri:excursion_set_map_id",
label="Excursion Set Map",
location="ExcursionSet.nii.gz",
format="image/nifti",
filename="ExcursionSet.nii.gz",
cluster_label_map_id="niiri:cluster_label_map_id",
max_intensity_projection_id="niiri:maximum_intensity_projection\
_id",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="d96b82761c299a66978893cab6034f3f8aed25d0a135636b0ffe79f4cf11b\
ecce86ba261f7aeb43717f5d0e47ad0b14cfb0402786251e3f2c507890c83b27652",
num_of_clusters="5",
p_value="2.83510681598e-09",
inference_id="niiri:inference_id"
),
"Image": dict(
image_id="niiri:maximum_intensity_projection_id",
location="MaximumIntensityProjection.png",
filename="MaximumIntensityProjection.png",
format="image/png"
),
"ClusterLabelsMap": dict(
cluster_label_map_id="niiri:cluster_label_map_id",
location="ClusterLabels.nii.gz",
filename="ClusterLabels.nii.gz",
format="image/nifti"
),
"SupraThresholdCluster-1": dict(
cluster_id="niiri:supra_threshold_cluster_0001",
label="Supra-Threshold Cluster: 0001",
cluster_size_in_voxels="839",
cluster_label_id="1",
cluster_size_in_resels="6.31265696809113",
p_value_unc="3.55896824480477e-19",
p_value_fwe="0",
p_value_fdr="1.77948412240239e-18",
excursion_set_id="niiri:excursion_set_map_id"
),
"SupraThresholdCluster-2": dict(
cluster_id="niiri:supra_threshold_cluster_0002",
label="Supra-Threshold Cluster: 0002",
cluster_size_in_voxels="695",
cluster_label_id="2",
cluster_size_in_resels="5.22919736927692",
p_value_unc="5.34280282632073e-17",
p_value_fwe="0",
p_value_fdr="1.33570070658018e-16",
excursion_set_id="niiri:excursion_set_map_id"
),
"SupraThresholdCluster-3": dict(
cluster_id="niiri:supra_threshold_cluster_0003",
label="Supra-Threshold Cluster: 0003",
cluster_size_in_voxels="37",
cluster_label_id="3",
cluster_size_in_resels="0.278388924695318",
p_value_unc="0.00497953247554004",
p_value_fwe="0.000255384009130943",
p_value_fdr="0.00829922079256674",
excursion_set_id="niiri:excursion_set_map_id"
),
"SupraThresholdCluster-4": dict(
cluster_id="niiri:supra_threshold_cluster_0004",
label="Supra-Threshold Cluster: 0004",
cluster_size_in_voxels="29",
cluster_label_id="4",
cluster_size_in_resels="0.218196724761195",
p_value_unc="0.0110257032104773",
p_value_fwe="0.000565384750377596",
p_value_fdr="0.0137821290130967",
excursion_set_id="niiri:excursion_set_map_id"
),
"SupraThresholdCluster-5": dict(
cluster_id="niiri:supra_threshold_cluster_0005",
label="Supra-Threshold Cluster: 0005",
cluster_size_in_voxels="12",
cluster_label_id="5",
cluster_size_in_resels="0.0902882999011843",
p_value_unc="0.0818393184514307",
p_value_fwe="0.00418900977248904",
p_value_fdr="0.0818393184514307",
excursion_set_id="niiri:excursion_set_map_id"
),
"Peak_ValueP-1": dict(
peak_id="niiri:peak_0001",
label="Peak: 0001",
location="niiri:coordinate_0001",
value="17.5207633972168",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="1.19156591713838e-11",
cluster_id="niiri:supra_threshold_cluster_0001"
),
"Coordinate-1": dict(
coordinate_id="niiri:coordinate_0001",
label="Coordinate: 0001",
coord="[ -60, -25, 11 ]"
),
"Peak_ValueP-2": dict(
peak_id="niiri:peak_0002",
label="Peak: 0002",
location="niiri:coordinate_0002",
value="13.0321407318",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="1.19156591714e-11",
cluster_id="niiri:supra_threshold_cluster_0001"
),
"Coordinate-2": dict(
coordinate_id="niiri:coordinate_0002",
label="Coordinate: 0002",
coord="[ -42, -31, 11 ]"
),
"Peak_ValueP-3": dict(
peak_id="niiri:peak_0003",
label="Peak: 0003",
location="niiri:coordinate_0003",
value="10.2856016159058",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="7.69451169446711e-12",
p_value_fdr="6.84121260274992e-10",
cluster_id="niiri:supra_threshold_cluster_0001"
),
"Coordinate-3": dict(
coordinate_id="niiri:coordinate_0003",
label="Coordinate: 0003",
coord="[ -66, -31, -1 ]"
),
"Peak_ValueP-4": dict(
peak_id="niiri:peak_0004",
label="Peak: 0004",
location="niiri:coordinate_0004",
value="13.5425577163696",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="1.19156591713838e-11",
cluster_id="niiri:supra_threshold_cluster_0002"
),
"Coordinate-4": dict(
coordinate_id="niiri:coordinate_0004",
label="Coordinate: 0004",
coord="[ 63, -13, -4 ]"
)
}
NIDM_SPM_DIR = os.path.join(os.path.dirname(
os.path.dirname(os.path.abspath(__file__))), 'spm', "example003")
ttl_file = os.path.join(NIDM_SPM_DIR, 'spm_results_conjunction.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def main():
nidm_classes = {
"ImagingInstrument":
dict(
id="niiri:mr_scanner_id",
label="MRI Scanner",
type=q_graph.qname(NLX_MRI_SCANNER),
),
"DesignMatrix":
dict(design_matrix_id='niiri:design_matrix_id',
label="Design Matrix",
location="DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id"),
"Image-DesignMatrix":
dict(image_id="niiri:design_matrix_png_id",
location="DesignMatrix.png",
filename="DesignMatrix.png",
format="image/png"),
"Group":
dict(id="niiri:group_id",
label="Group: Control",
name="Control",
numsubjects="23"),
"Group-2":
dict(id="niiri:group2_id",
label="Group: Patient",
name="Patient",
numsubjects="21"),
"Data_wasAttributedTo":
dict(data_id='niiri:data_id',
label="Data",
scaling="true",
target=100,
scanner_id="niiri:mr_scanner_id",
sub_or_group_id="niiri:group_id",
group2_id="niiri:group2_id",
mr_protocol=q_graph.qname(NLX_FMRI_PROTOCOL)),
"ErrorModel":
dict(error_model_id="niiri:error_model_id",
noise_distribution="obo:STATO_0000227",
variance_homo="true",
variance_spatial="nidm:NIDM_0000073",
dependence="nidm:NIDM_0000048",
dependence_spatial="nidm:NIDM_0000073"),
"ModelParametersEstimation":
dict(model_pe_id="niiri:model_pe_id",
label="Model parameters estimation",
est_method=STATO_OLS_STR,
est_method_comment=STATO_OLS_LABEL,
design_matrix_id="niiri:design_matrix_id",
data_matrix_id="niiri:data_id",
error_model_id="niiri:error_model_id",
software_id="niiri:software_id"),
"ParameterEstimateMap_Location-1":
dict(beta_map_id="niiri:beta_map_id_1",
label="Beta Map 1",
location="ParameterEstimate_0001.nii.gz",
filename="ParameterEstimate_0001.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_pe_id"),
"DerivedMap-PE1":
dict(derived_from_map_id="niiri:beta_map_id_1_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0001.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a",
map_id="niiri:beta_map_id_1"),
"ParameterEstimateMap_Location-2":
dict(beta_map_id="niiri:beta_map_id_2",
label="Beta Map 2",
location="ParameterEstimate_0002.nii.gz",
filename="ParameterEstimate_0002.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_pe_id"),
"DerivedMap-PE2":
dict(derived_from_map_id="niiri:beta_map_id_2_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0002.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a",
map_id="niiri:beta_map_id_2"),
"ParameterEstimateMap_Location-3":
dict(beta_map_id="niiri:beta_map_id_3",
label="Beta Map 3",
location="ParameterEstimate_0003.nii.gz",
filename="ParameterEstimate_0003.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_pe_id"),
"DerivedMap-PE3":
dict(derived_from_map_id="niiri:beta_map_id_3_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0003.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a",
map_id="niiri:beta_map_id_3"),
"CoordinateSpace-1":
dict(
coordinate_space_id="niiri:coordinate_space_id_1",
label="Coordinate space 1",
voxel_to_world_mapping="[[-3, 0, 0, 78],[0, 3, 0, -112],[0, 0, 3, \
-50],[0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000051",
number_of_dim="3",
dimensions="[ 53, 63, 46 ]"),
"ResidualMeanSquaresMap":
dict(residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
label="Residual Mean Squares Map",
location="ResidualMeanSquares.nii.gz",
filename="ResidualMeanSquares.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_pe_id"),
"MaskMap_Analysis":
dict( # The analysis mask
mask_id="niiri:mask_id_1",
label="Mask",
location="Mask.nii.gz",
filename="Mask.nii.gz",
user_defined="false",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
generated_by_act_id="niiri:model_pe_id",
# fixme: also used by niiri:contrast_estimation_id_2
used_by_act_id="niiri:contrast_estimation_id"),
"ContrastWeights":
dict(contrast_id="niiri:contrast_id",
label="Contrast: listening > reading",
value="[1, -1, 0, 0]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > reading"),
"ContrastWeights-2":
dict(contrast_id="niiri:contrast_id_2",
label="Contrast: motor",
value="[ 0, 0, 1 ]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="motor"),
"ContrastEstimation":
dict(contrast_estimation_id="niiri:contrast_estimation_id",
label="Contrast estimation 1",
software_id="niiri:software_id",
mask_id="niiri:mask_id_1",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id",
param_est_map="niiri:beta_map_id_1"),
"ContrastEstUsedParamEst-Con1PE2":
dict(contrast_estimation_id="niiri:contrast_estimation_id",
param_est_map="niiri:beta_map_id_2"),
"ContrastEstimation-2":
dict(contrast_estimation_id="niiri:contrast_estimation_id_2",
label="Contrast estimation 2",
software_id="niiri:software_id",
mask_id="niiri:mask_id_1",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id_2",
param_est_map="niiri:beta_map_id_3"),
"ContrastEstUsedParamEst-Con2PE3":
dict(contrast_estimation_id="niiri:contrast_estimation_id_2",
param_est_map="niiri:beta_map_id_3"),
"ContrastMap":
dict(contrast_map_id="niiri:contrast_map_id",
label="Contrast Map: listening > reading",
location="Contrast_0001.nii.gz",
format="image/nifti",
filename="Contrast_0001.nii.gz",
contrast_name="listening > reading",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
contrast_est_id="niiri:contrast_estimation_id"),
"ContrastMap-2":
dict(contrast_map_id="niiri:contrast_map_id_2",
label="Contrast Map: motor",
location="Contrast_0002.nii.gz",
format="image/nifti",
filename="Contrast_0002.nii.gz",
contrast_name="motor",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
contrast_est_id="niiri:contrast_estimation_id_2"),
"DerivedMap-ContrastMap-2":
dict(derived_from_map_id="niiri:contrast_map_id_2_der",
derived_map_type="nidm:NIDM_0000002",
filename="con_0002.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a",
map_id="niiri:contrast_map_id_2"),
"ContrastStandardErrorMap":
dict(
contrast_standard_error_map_id="niiri:contrast_standard_error_map_\
id",
label="Contrast 1 Standard Error Map",
location="ContrastStandardError_0001.nii.gz",
format="image/nifti",
filename="ContrastStandardError_0001.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
contrast_est_id="niiri:contrast_estimation_id"),
"ContrastStandardErrorMap-2":
dict(
contrast_standard_error_map_id="niiri:contrast_standard_error_map_\
id_2",
label="Contrast 2 Standard Error Map",
location="ContrastStandardError_0002.nii.gz",
format="image/nifti",
filename="ContrastStandardError_0002.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
contrast_est_id="niiri:contrast_estimation_id_2"),
"StatisticMap_T":
dict(statistic_map_id="niiri:statistic_map_id",
label="Statistic Map: listening > reading",
location="TStatistic_0001.nii.gz",
format="image/nifti",
filename="TStatistic_0001.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > reading",
error_dof="72.9999999990787",
effect_dof="1",
sha="e43b6e01b0463fe7d40782137867a",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id"),
"DerivedMap-StatMap":
dict(derived_from_map_id="niiri:statistic_map_id_der",
derived_map_type="nidm:NIDM_0000076",
filename="spmT_0001.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a",
map_id="niiri:statistic_map_id"),
"StatisticMap_T-2":
dict(statistic_map_id="niiri:statistic_map_id_2",
label="Statistic Map: motor",
location="TStatistic_0002.nii.gz",
format="image/nifti",
filename="TStatistic_0002.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="motor",
error_dof="72.9999999990787",
effect_dof="1",
sha="e43b6e01b0463fe7d40782137867a",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id_2"),
"DerivedMap-StatMap-2":
dict(derived_from_map_id="niiri:statistic_map_id_2_der",
derived_map_type="nidm:NIDM_0000076",
filename="spmT_0002.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a",
map_id="niiri:statistic_map_id_2"),
"HeightThreshold_equivThresh_equivThresh2":
dict(height_threshold_id="niiri:height_threshold_id",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
label="Height Threshold: p<7.62276079258051e-07 (unc)",
value="7.62276079258051e-07",
equiv_thresh="niiri:height_threshold_id_2",
equiv_thresh2="niiri:height_threshold_id_3"),
"HeightThreshold-2":
dict(height_threshold_id="niiri:height_threshold_id_2",
thresh_type=OBO_STATISTIC_QNAME,
label="Height Threshold",
value="5.23529984739211"),
"HeightThreshold-3":
dict(
height_threshold_id="niiri:height_threshold_id_3",
thresh_type=OBO_P_VALUE_FWER_QNAME,
label="Height Threshold",
value="0.05",
),
"ExtentThresholdStat_equivThresh_equivThresh2_clusterSizeResels":
dict(extent_threshold_id="niiri:extent_threshold_id",
label="Extent Threshold: k>=10",
cluster_size_vox="10",
cluster_size_resels="3.3",
equiv_thresh="niiri:height_threshold_id_2",
equiv_thresh2="niiri:height_threshold_id_3"),
"ExtentThreshold-2":
dict(
extent_threshold_id="niiri:extent_threshold_id_2",
label="Extent Threshold",
thresh_type=OBO_P_VALUE_FWER_QNAME,
value="1",
),
"ExtentThreshold-3":
dict(
extent_threshold_id="niiri:extent_threshold_id_3",
label="Extent Threshold",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
value="1",
),
"DisplayMaskMap":
dict(display_map_id="niiri:display_map_id",
label="Display Mask Map",
user_defined="true",
location="DisplayMask.nii.gz",
filename="DisplayMask.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a"),
"PeakDefinitionCriteria_MaxPeaks":
dict(peak_definition_criteria_id="niiri:peak_definition_criteria_id",
label="Peak Definition Criteria",
max_num_peaks="3",
min_dist_peaks="8.0"),
"ClusterDefinitionCriteria":
dict(
cluster_definition_criteria_id="niiri:cluster_definition_criteria_\
id",
label="Cluster Connectivity Criterion: 18",
connectivity="nidm:NIDM_0000128"),
"ConjunctionInference":
dict(conj_inference_id="niiri:inference_id",
label="Conjunction Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id_1="niiri:statistic_map_id",
stat_map_id_2="niiri:statistic_map_id_2",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
display_mask_id="niiri:display_map_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"),
"SearchSpaceMaskMap":
dict( # The "search space"
search_space_id="niiri:search_space_mask_id",
location="SearchSpaceMask.nii.gz",
filename="SearchSpaceMask.nii.gz",
label="Search Space Mask Map",
format="image/nifti",
user_defined="false",
coordinate_space_id="niiri:coordinate_space_id_1",
expected_num_voxels="4.02834655908613",
expected_num_clusters="0.0512932943875478",
height_critical_fwe05="4.85241745689539",
height_critical_fdr05="5.7639536857605",
smallest_size_fwe05="12",
smallest_size_fdr05="29",
search_vol_voxels="69306",
search_vol_units="1871262",
resel_size="132.907586178202",
search_vol_resels="467.07642343881",
search_vol_resels_geom="[7, 42.96312274763, 269.40914815306, \
467.07642343881]",
noise_fwhm_in_voxels="[ 5.41278985910694, 5.43638957240286, \
4.51666658877481 ]",
noise_fwhm_in_units="[ 16.2383695773208, 16.3091687172086, \
13.5499997663244 ]",
random_field_station="true",
sha="932fd9f0d55e9822748f4a9b35a0a7f0fe442f3e061e2eda48c2617a2938\
df50ea84deca8de0725641a0105b712a80a0c8931df9bdf3bef788b1041379d00875",
inference_id="niiri:inference_id"),
"DerivedMap-Contrast":
dict(derived_from_map_id="niiri:contrast_map_id_der",
derived_map_type="nidm:NIDM_0000002",
filename="con_0001.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a",
map_id="niiri:contrast_map_id"),
"NIDMBundle":
dict(bundle_id="niiri:spm_results_id",
label="NIDM-Results",
object_model="nidm:NIDM_0000027",
version="1.1.0",
time="2014-05-19T10:30:00.000+01:00",
export_id="niiri:export_id"),
"SPM_ReselsPerVoxelMap":
dict(resels_per_voxel_map_id="niiri:resels_per_voxel_map_id",
label="Resels per Voxel Map",
location="ReselsPerVoxel.nii.gz",
filename="ReselsPerVoxel.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
model_pe_id="niiri:model_pe_id"),
"SPM_InferenceUsedRPVMap":
dict(inference_id="niiri:inference_id",
resels_per_voxel_map_id="niiri:resels_per_voxel_map_id"),
"DerivedMap-RPV":
dict(derived_from_map_id="niiri:resels_per_voxel_map_id_der",
derived_map_type="nidm:NIDM_0000144",
filename="RPV.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a",
map_id="niiri:resels_per_voxel_map_id"),
"SPM_Software":
dict(software_id="niiri:software_id",
software_type="scr:SCR_007037",
label="SPM",
version="12b.5853"),
"GrandMeanMap":
dict(grand_mean_map_id="niiri:grand_mean_map_id",
label="Grand Mean Map",
location="GrandMean.nii.gz",
filename="GrandMean.nii.gz",
format="image/nifti",
masked_median="115",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
model_pe_id="niiri:model_pe_id"),
"ExporterSoftware":
dict(software_id="niiri:exporter_id",
software_type="nidm:NIDM_0000168",
label="spm_results_nidm",
version="12b.5858"),
"Export":
dict(export_id="niiri:export_id",
label="NIDM-Results export",
exporter_id="niiri:exporter_id"),
"ExcursionSetMap":
dict(
id="niiri:excursion_set_map_id",
label="Excursion Set Map",
location="ExcursionSet.nii.gz",
format="image/nifti",
filename="ExcursionSet.nii.gz",
cluster_label_map_id="niiri:cluster_label_map_id",
max_intensity_projection_id="niiri:maximum_intensity_projection\
_id",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="d96b82761c299a66978893cab6034f3f8aed25d0a135636b0ffe79f4cf11b\
ecce86ba261f7aeb43717f5d0e47ad0b14cfb0402786251e3f2c507890c83b27652",
num_of_clusters="5",
p_value="2.83510681598e-09",
inference_id="niiri:inference_id"),
"Image":
dict(image_id="niiri:maximum_intensity_projection_id",
location="MaximumIntensityProjection.png",
filename="MaximumIntensityProjection.png",
format="image/png"),
"ClusterLabelsMap":
dict(cluster_label_map_id="niiri:cluster_label_map_id",
location="ClusterLabels.nii.gz",
filename="ClusterLabels.nii.gz",
format="image/nifti"),
"SupraThresholdCluster-1":
dict(cluster_id="niiri:supra_threshold_cluster_0001",
label="Supra-Threshold Cluster: 0001",
cluster_size_in_voxels="839",
cluster_label_id="1",
cluster_size_in_resels="6.31265696809113",
p_value_unc="3.55896824480477e-19",
p_value_fwe="0",
p_value_fdr="1.77948412240239e-18",
excursion_set_id="niiri:excursion_set_map_id"),
"SupraThresholdCluster-2":
dict(cluster_id="niiri:supra_threshold_cluster_0002",
label="Supra-Threshold Cluster: 0002",
cluster_size_in_voxels="695",
cluster_label_id="2",
cluster_size_in_resels="5.22919736927692",
p_value_unc="5.34280282632073e-17",
p_value_fwe="0",
p_value_fdr="1.33570070658018e-16",
excursion_set_id="niiri:excursion_set_map_id"),
"SupraThresholdCluster-3":
dict(cluster_id="niiri:supra_threshold_cluster_0003",
label="Supra-Threshold Cluster: 0003",
cluster_size_in_voxels="37",
cluster_label_id="3",
cluster_size_in_resels="0.278388924695318",
p_value_unc="0.00497953247554004",
p_value_fwe="0.000255384009130943",
p_value_fdr="0.00829922079256674",
excursion_set_id="niiri:excursion_set_map_id"),
"SupraThresholdCluster-4":
dict(cluster_id="niiri:supra_threshold_cluster_0004",
label="Supra-Threshold Cluster: 0004",
cluster_size_in_voxels="29",
cluster_label_id="4",
cluster_size_in_resels="0.218196724761195",
p_value_unc="0.0110257032104773",
p_value_fwe="0.000565384750377596",
p_value_fdr="0.0137821290130967",
excursion_set_id="niiri:excursion_set_map_id"),
"SupraThresholdCluster-5":
dict(cluster_id="niiri:supra_threshold_cluster_0005",
label="Supra-Threshold Cluster: 0005",
cluster_size_in_voxels="12",
cluster_label_id="5",
cluster_size_in_resels="0.0902882999011843",
p_value_unc="0.0818393184514307",
p_value_fwe="0.00418900977248904",
p_value_fdr="0.0818393184514307",
excursion_set_id="niiri:excursion_set_map_id"),
"Peak_ValueP-1":
dict(peak_id="niiri:peak_0001",
label="Peak: 0001",
location="niiri:coordinate_0001",
value="17.5207633972168",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="1.19156591713838e-11",
cluster_id="niiri:supra_threshold_cluster_0001"),
"Coordinate-1":
dict(coordinate_id="niiri:coordinate_0001",
label="Coordinate: 0001",
coord="[ -60, -25, 11 ]"),
"Peak_ValueP-2":
dict(peak_id="niiri:peak_0002",
label="Peak: 0002",
location="niiri:coordinate_0002",
value="13.0321407318",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="1.19156591714e-11",
cluster_id="niiri:supra_threshold_cluster_0001"),
"Coordinate-2":
dict(coordinate_id="niiri:coordinate_0002",
label="Coordinate: 0002",
coord="[ -42, -31, 11 ]"),
"Peak_ValueP-3":
dict(peak_id="niiri:peak_0003",
label="Peak: 0003",
location="niiri:coordinate_0003",
value="10.2856016159058",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="7.69451169446711e-12",
p_value_fdr="6.84121260274992e-10",
cluster_id="niiri:supra_threshold_cluster_0001"),
"Coordinate-3":
dict(coordinate_id="niiri:coordinate_0003",
label="Coordinate: 0003",
coord="[ -66, -31, -1 ]"),
"Peak_ValueP-4":
dict(peak_id="niiri:peak_0004",
label="Peak: 0004",
location="niiri:coordinate_0004",
value="13.5425577163696",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="1.19156591713838e-11",
cluster_id="niiri:supra_threshold_cluster_0002"),
"Coordinate-4":
dict(coordinate_id="niiri:coordinate_0004",
label="Coordinate: 0004",
coord="[ 63, -13, -4 ]")
}
NIDM_SPM_DIR = os.path.join(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'spm',
"example003")
ttl_file = os.path.join(NIDM_SPM_DIR, 'spm_results_conjunction.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def main():
nidm_classes = {
"NIDMBundle": dict(
comment="NIDM-Results Bundle",
bundle_id="niiri:nidm_results_id",
label="NIDM-Results",
object_model="nidm:NIDM_0000027",
version="1.1.0",
time="2014-05-19T10:30:00.000+01:00",
export_id="niiri:export_id"
),
"SPM_Software": dict(
software_id="niiri:spm_software_id",
software_type="scr:SCR_007037",
label="SPM",
version="8.6225"
),
"FSL_Software": dict(
software_id="niiri:software_id",
software_type="scr:SCR_002823",
label="FSL",
version="5.0.1",
feat_version="6.00"
),
"ExporterSoftware-FSL": dict(
software_id="niiri:exporter_id",
software_type="nidm:NIDM_0000167",
label="nidmfsl",
version="0.2.0"
),
"Export": dict(
export_id="niiri:export_id",
label="NIDM-Results export",
exporter_id="niiri:exporter_id"
),
"ExporterSoftware-SPM": dict(
software_id="niiri:exporter_id",
software_type="nidm:NIDM_0000168",
label="spm_results_nidm",
version="12b.5858"
),
"DesignMatrix": dict(
comment="Design Matrix: Group Level",
design_matrix_id='niiri:design_matrix_id',
label="Design Matrix",
location="DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id"),
"DesignMatrix_1stLevel": dict(
comment="Design Matrix: Subject Level",
design_matrix_id='niiri:first_level_design_matrix_id',
label="First-Level Design Matrix",
location="DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id",
hrf_basis="niiri:hrf_basis_id",
drift_model="niiri:drift_model_id",
regressors="[\\\"Sn(1) active*bf(1)\\\",\\\"Sn(1) constant\\\"]"),
"DesignMatrix_1stLevel-FIR": dict(
comment="HRF: FIR Basis Set",
design_matrix_id='niiri:first_level_design_matrix_id',
label="First-Level Design Matrix",
location="DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id",
hrf_basis=NIDM_FINITE_IMPULSE_RESPONSE_HRB,
drift_model="niiri:drift_model_id",
regressors="[\\\"Sn(1) active*bf(1)\\\",\\\"Sn(1) constant\\\"]"),
"DesignMatrix_1stLevel_HRFBasis2_HRFBasis3-InformedBasisSet": dict(
comment="HRF: SPM's Informed Basis Set",
design_matrix_id='niiri:first_level_design_matrix_id',
label="First-Level Design Matrix",
location="DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id",
hrf_basis=SPM_CANONICAL_HRF,
hrf_basis_2=SPM_TEMPORAL_DERIVATIVE,
hrf_basis_3=SPM_DISPERSION_DERIVATIVE,
drift_model="niiri:drift_model_id",
regressors="[\\\"Sn(1) active*bf(1)\\\",\\\"Sn(1) constant\\\"]"),
"Map_atLocation-nii": dict(
comment="Map: One-file Nifti (.nii)",
map_type="nidm:NIDM_0000052",
map_id="niiri:map_id",
filename='image.nii',
coordinate_space_id="niiri:coordinate_space_id",
sha="e43b6e01b0463fe7d40782137867ae43b6e01b0463fe7d40782137867a",
location="image.nii"),
"Map_atLocation_hasMapHeader-img": dict(
comment="Map: Nifti (.img)",
map_type="nidm:NIDM_0000052",
map_id="niiri:map_id",
filename='image.img',
coordinate_space_id="niiri:coordinate_space_id",
sha="e43b6e01b0463fe7d40782137867ae43b6e01b0463fe7d40782137867a",
map_header="niiri:map_header_id",
location="image.img"),
"MapHeader": dict(
comment="Map Header: Nifti header (.hdr)",
map_header_id="niiri:map_header_id",
filename='image.hdr',
sha="e43b6e01b0463fe7d40782137867ae43b6e01b0463fe7d40782137867a",
location="image.hdr"),
"Image-DesignMatrix": dict(
comment="Image: Design Matrix",
image_id="niiri:design_matrix_png_id",
location="DesignMatrix.png",
filename="DesignMatrix.png",
format="image/png"
),
"Group": dict(
comment="Group: Control group with 23 subjects",
id="niiri:group_id",
label="Group: Control",
name="Control",
numsubjects="23"
),
"Data_wasAttributedTo": dict(
comment="Data",
data_id='niiri:data_id',
label="Data",
scaling="true",
target=100,
scanner_id="niiri:my_scanner_id",
sub_or_group_id="niiri:group_id",
group2_id="niiri:group2_id",
mr_protocol=q_graph.qname(NLX_FMRI_PROTOCOL),
),
"ImagingInstrument": dict(
id="niiri:mr_scanner_id",
label="MRI Scanner",
type=q_graph.qname(NLX_MRI_SCANNER),
),
"ErrorModel-OLS": dict(
comment="Error Model: Ordinary least squares",
error_model_id="niiri:error_model_id",
noise_distribution=STATO_GAUSSIAN_DISTRIBUTION,
variance_homo="true",
variance_spatial=NIDM_SPATIALLY_LOCAL_MODEL,
dependence=NIDM_INDEPENDENT_ERROR,
dependence_spatial=NIDM_SPATIALLY_LOCAL_MODEL
),
"ErrorModel-WLS": dict(
comment="Error Model: Weighted least squares",
error_model_id="niiri:error_model_id",
noise_distribution=STATO_GAUSSIAN_DISTRIBUTION,
variance_homo="false",
variance_spatial=NIDM_SPATIALLY_LOCAL_MODEL,
dependence=NIDM_INDEPENDENT_ERROR,
dependence_spatial=NIDM_SPATIALLY_LOCAL_MODEL
),
"ErrorModel-SPMnonSphericity": dict(
comment="Error Model: SPM non sphericity",
error_model_id="niiri:error_model_id",
noise_distribution=STATO_GAUSSIAN_DISTRIBUTION,
variance_homo="false",
variance_spatial=NIDM_SPATIALLY_LOCAL_MODEL,
dependence=STATO_UNSTRUCTURED_COVARIANCE,
dependence_spatial=NIDM_SPATIALLY_GLOBAL_MODEL
),
"ModelParametersEstimation": dict(
comment="Model Parameters Estimation",
model_pe_id="niiri:model_pe_id",
label="Model parameters estimation",
est_method=STATO_OLS_STR,
est_method_comment=STATO_OLS_LABEL,
software_id="niiri:software_id",
design_matrix_id="niiri:design_matrix_id",
data_matrix_id="niiri:data_id",
error_model_id="niiri:error_model_id"
),
"ParameterEstimateMap": dict(
comment="Parameter Estimate Map",
beta_map_id="niiri:beta_map_id_1",
label="Beta Map 1",
location="ParameterEstimate_0001.nii.gz",
filename="ParameterEstimate_0001.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_pe_id"),
"ResidualMeanSquaresMap": dict(
comment="Residual Mean Squares Map",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
label="Residual Mean Squares Map",
location="ResidualMeanSquares.nii.gz",
filename="ResidualMeanSquares.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_pe_id"),
"MaskMap": dict(
comment="Mask Map",
mask_id="niiri:mask_id_2",
user_defined="false",
label="Mask",
location="Mask.nii.gz",
filename="Mask.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
used_by_act_id="niiri:model_pe_id"),
"ContrastWeights": dict(
comment="Contrast Weights",
contrast_id="niiri:contrast_id",
label="Contrast: Listening > Rest",
value="[ 1, 0, 0 ]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > rest"),
"ContrastEstimation": dict(
comment="Contrast Estimation",
contrast_estimation_id="niiri:contrast_estimation_id",
label="Contrast estimation",
software_id="niiri:software_id",
mask_id="niiri:mask_id_2",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id",
param_est_map="niiri:beta_map_id_1"),
"ContrastMap": dict(
comment="Contrast Map",
contrast_map_id="niiri:contrast_map_id",
label="Contrast Map: listening > rest",
location="Contrast.nii.gz",
format="image/nifti",
filename="Contrast.nii.gz",
contrast_name="listening > rest",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
contrast_est_id="niiri:contrast_estimation_id"),
"ContrastStandardErrorMap": dict(
comment="Contrast Standard Error Map",
contrast_standard_error_map_id="niiri:contrast_standard_error_map_\
id",
label="Contrast Standard Error Map",
location="ContrastStandardError.nii.gz",
format="image/nifti",
filename="ContrastStandardError.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
contrast_est_id="niiri:contrast_estimation_id"),
"StatisticMap-T": dict(
comment="Statistic Map: T",
statistic_map_id="niiri:statistic_map_id",
label="Statistic Map: listening > rest",
location="TStatistic.nii.gz",
format="image/nifti",
filename="TStatistic.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > rest",
error_dof="72.9999999990787",
effect_dof="1",
sha="e43b6e01b0463fe7d40782137867a",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id"),
"HeightThreshold_equivThresh-FWER": dict(
comment="Height Threshold: p<0.05 FWER",
height_threshold_id="niiri:height_threshold_fwer_id",
label="Height Threshold: p<0.05 (FWER-corrected)",
value="0.05",
thresh_type=OBO_P_VALUE_FWER_QNAME,
equiv_thresh="niiri:height_threshold_stat_id"
),
"HeightThreshold-Stat": dict(
comment="Height Threshold: Z<0.0000000672357409",
height_threshold_id="niiri:height_threshold_stat_id",
label="Height Threshold: Z<0.0000000672357409",
value="0.0000000672357409",
thresh_type=OBO_STATISTIC_QNAME,
),
"HeightThreshold-FDR": dict(
comment="Height Threshold: p<0.05 FDR",
height_threshold_id="niiri:height_threshold_fdr_id",
label="Height Threshold: p<0.05 (FDR-corrected)",
value="0.05",
thresh_type=OBO_Q_VALUE_FDR_QNAME
),
"HeightThreshold-Unc": dict(
comment="Height Threshold: p<0.001 uncorrected",
height_threshold_id="niiri:height_threshold_unc_id",
label="Height Threshold: p<0.001 (uncorrected)",
value="0.001",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME
),
"ExtentThresholdStat_clusterSizeResels": dict(
comment="Extent Threshold: k>=0",
extent_threshold_id="niiri:extent_threshold_stat_id",
label="Extent Threshold: k>=0",
cluster_size_vox="0",
cluster_size_resels="0",
),
"ExtentThreshold_equivThresh-FWER": dict(
comment="Extent Threshold: p<0.05 FWER",
extent_threshold_id="niiri:extent_threshold_fwer_id",
thresh_type=OBO_P_VALUE_FWER_QNAME,
label="Extent Threshold: p<0.05 (FWER-corrected)",
value="0.05",
equiv_thresh="niiri:extent_threshold_stat_id"
),
"ExtentThreshold-FDR": dict(
comment="Extent Threshold: p<0.05 FDR",
extent_threshold_id="niiri:extent_threshold_fdr_id",
thresh_type=OBO_Q_VALUE_FDR_QNAME,
label="Extent Threshold: p<0.05 (FDR-corrected)",
value="0.05"
),
"ExtentThreshold-Unc": dict(
comment="Extent Threshold: p<0.001 uncorrected",
extent_threshold_id="niiri:extent_threshold_unc_id",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
label="Extent Threshold: p<0.001 (uncorrected)",
value="0.001"
),
"SPM_ReselsPerVoxelMap": dict(
comment="Resels per Voxel Map",
resels_per_voxel_map_id="niiri:resels_per_voxel_map_id",
label="Resels per Voxel Map",
location="ReselsPerVoxel.nii.gz",
filename="ReselsPerVoxel.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
model_pe_id="niiri:model_pe_id"
),
"ClusterLabelsMap": dict(
comment="Cluster Labels Map",
cluster_label_map_id="niiri:cluster_label_map_id",
location="ClusterLabels.nii.gz",
filename="ClusterLabels.nii.gz",
format="image/nifti"
),
"DisplayMaskMap": dict(
comment="Display Mask Map",
display_map_id="niiri:display_map_id",
label="Display Mask Map",
location="DisplayMask.nii.gz",
filename="DisplayMask.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_2",
sha="e43b6e01b0463fe7d40782137867a"
),
"PeakDefinitionCriteria_MaxPeaks": dict(
comment="Peak Definition Criteria",
peak_definition_criteria_id="niiri:peak_definition_criteria_id",
label="Peak Definition Criteria",
max_num_peaks="3",
min_dist_peaks="8.0"
),
"Inference-OneTailed": dict(
comment="Inference: one-tailed",
inference_id="niiri:inference_id",
label="Inference",
alternative_hyp=NIDM_ONE_TAILED_TEST,
stat_map_id="niiri:statistic_map_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
inference_mask_id="niiri:mask_id_3",
display_mask_id="niiri:display_map_id",
mask_id="niiri:mask_id",
software_id="niiri:software_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id"
),
"Inference-TwoTailed": dict(
comment="Inference: two-tailed",
inference_id="niiri:inference_id",
label="Inference",
alternative_hyp=NIDM_TWO_TAILED_TEST,
stat_map_id="niiri:statistic_map_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
inference_mask_id="niiri:mask_id_3",
display_mask_id="niiri:display_map_id",
mask_id="niiri:mask_id",
software_id="niiri:software_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id"
),
"ConjunctionInference": dict(
comment="Conjunction Inference",
conj_inference_id="niiri:inference_id",
label="Conjunction Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id_1="niiri:statistic_map_id",
stat_map_id_2="niiri:statistic_map_id_2",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
display_mask_id="niiri:display_map_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"
),
"SPM_KConjunctionInference": dict(
comment="SPM's Partial Conjunction Inference",
conj_inference_id="niiri:conjunction_id_2",
label="SPM's Partial Conjunction Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id_1="niiri:statistic_map_id_1",
stat_map_id_2="niiri:statistic_map_id_2",
global_null_degree="1",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
display_mask_id="niiri:display_map_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"
),
"ExcursionSetMap": dict(
comment="Excursion Set Map",
id="niiri:excursion_set_map_id",
label="Excursion Set Map",
location="ExcursionSet.nii.gz",
format="image/nifti",
filename="ExcursionSet.nii.gz",
cluster_label_map_id="niiri:cluster_label_map_id",
max_intensity_projection_id="niiri:maximum_intensity_projection_\
id",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
num_of_clusters="8",
p_value="8.95949980872501e-14",
inference_id="niiri:inference_id"
),
"SupraThresholdCluster": dict(
comment="Supra-Threshold Cluster",
cluster_id="niiri:supra_threshold_cluster_0001",
label="Supra-Threshold Cluster 0001",
cluster_size_in_voxels="530",
cluster_label_id="1",
cluster_size_in_resels="23.1209189500945",
p_value_unc="9.56276736481136e-52",
p_value_fwe="0",
p_value_fdr="7.65021389184909e-51",
excursion_set_id="niiri:excursion_set_map_id"
),
"Peak_ValueP": dict(
comment="Peak",
peak_id="niiri:peak_0001",
label="Peak 0001",
location="niiri:coordinate_0001",
value="13.9346199035645",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="6.3705194444993e-11",
cluster_id="niiri:supra_threshold_cluster_0001"
),
"Coordinate": dict(
comment="Coordinate",
coordinate_id="niiri:coordinate_0001",
label="Coordinate: 0001",
coord="[ -60, -28, 13 ]"
),
"SearchSpaceMaskMap": dict(
comment="Search Space Mask Map",
search_space_id="niiri:search_space_mask_id",
location="SearchSpaceMask.nii.gz",
filename="SearchSpaceMask.nii.gz",
label="Search Space Mask Map",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_2",
expected_num_voxels="0.553331387916112",
expected_num_clusters="0.0889172687960151",
height_critical_fwe05="5.23529984739211",
height_critical_fdr05="6.22537899017334",
smallest_size_fwe05="1",
smallest_size_fdr05="3",
search_vol_voxels="65593",
search_vol_units="1771011",
resel_size="22.9229643140043",
search_vol_resels="2552.68032521656",
search_vol_resels_geom="[3, 72.3216126440484, 850.716735116472, \
2552.68032521656]",
noise_fwhm_in_voxels="[ 2.95881189165801, 2.96628446669584, \
2.61180425626264 ]",
noise_fwhm_in_units="[ 8.87643567497404, 8.89885340008753, \
7.83541276878791 ]",
random_field_station="false",
sha="e43b6e01b0463fe7d40782137867a",
inference_id="niiri:inference_id"
),
"FSL_ClusterCenterOfGravity": dict(
comment="Cluster Center Of Gravity",
center_of_gravity_id="niiri:center_of_gravity_1",
location="niiri:coordinate_0001",
label="Center of gravity",
cluster_id="niiri:supra_threshold_cluster_0001",
),
"CoordinateSpace": dict(
comment="Coordinate Space",
coordinate_space_id="niiri:coordinate_space_id_1",
label="Coordinate space 1",
voxel_to_world_mapping="[[-3, 0, 0, 78],[0, 3, 0, -112],\
[0, 0, 3, -50],[0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000051",
number_of_dim="3",
dimensions="[ 53, 63, 46 ]"),
"Image": dict(
comment="Image",
image_id="niiri:maximum_intensity_projection_id",
location="MaximumIntensityProjection.png",
filename="MaximumIntensityProjection.png",
format="image/png"
),
"GrandMeanMap": dict(
comment="Grand Mean Map",
grand_mean_map_id="niiri:grand_mean_map_id",
label="Grand Mean Map",
location="GrandMean.nii.gz",
filename="GrandMean.nii.gz",
format="image/nifti",
masked_median="115",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
model_pe_id="niiri:model_pe_id"
),
"SPM_DriftModel": dict(
comment="SPM's DCT Drift Model",
id="niiri:drift_model_id",
label="SPM's DCT Drift Model",
cut_off="128"
),
"FSL_DriftModel": dict(
comment="FSL's Gaussian Running Line Drift Model",
id="niiri:drift_model_id",
label="FSL's Gaussian Running Line Drift Model",
cut_off="2"
),
"ClusterDefinitionCriteria-06": dict(
comment="Cluster connectivity: face",
cluster_definition_criteria_id="niiri:cluster_definition_criteria\
_id",
label="Cluster Connectivity Criterion: 6",
connectivity="nidm:NIDM_0000130"
),
"ClusterDefinitionCriteria-18": dict(
comment="Cluster connectivity: face or edge",
cluster_definition_criteria_id="niiri:cluster_definition_criteria\
_id",
label="Cluster Connectivity Criterion: 18",
connectivity="nidm:NIDM_0000128"
),
"ClusterDefinitionCriteria-26": dict(
comment="Cluster connectivity: face, edge or corner",
cluster_definition_criteria_id="niiri:cluster_definition_criteria\
_id",
label="Cluster Connectivity Criterion: 26",
connectivity="nidm:NIDM_0000129"
)
}
# Delete old examples
shutil.rmtree(EX_DIR)
os.mkdir(EX_DIR)
example = ExampleFromTemplate(nidm_classes, EX_DIR, True)
example.create_example()
def main():
nidm_classes = {
"ImagingInstrument":
dict(
id="niiri:mr_scanner_id",
label="MRI Scanner",
type=q_graph.qname(NLX_MRI_SCANNER),
),
"DesignMatrix_1stLevel":
dict(design_matrix_id='niiri:design_matrix_id',
label="Design Matrix",
location="DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id",
regressors="[\\\"Gen\\\", \\\"Gen*temporal_derivative\\\""
", \\\"Shad\\\", \\\"Shad*temporal_derivative\\\"]",
hrf_basis="fsl:FSL_0000001",
drift_model="niiri:drift_model_id"),
"FSL_DriftModel":
dict(id="niiri:drift_model_id",
label="FSL's Gaussian Running Line Drift Model",
cut_off="1908"),
"Image-DesignMatrix":
dict(image_id="niiri:design_matrix_png_id",
location="DesignMatrix.png",
filename="DesignMatrix.png",
format="image/png"),
"ClusterLabelsMap":
dict(
cluster_label_map_id="niiri:cluster_label_map_id",
label="Cluster Labels Map",
location="ClusterLabels.nii.gz",
filename="ClusterLabels.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="13093aae03897e2518307d000eb298f4b1439814d8d3d77c622b717423f93\
506dd5de5669513ab65c6dd74a7d27ee9df08620f546ed00575517b40e5878c2c96"),
"Person":
dict(id='niiri:subject_id', label="Person"),
"Data":
dict(data_id='niiri:data_id',
label="Data",
scaling="true",
target="10000",
scanner_id="niiri:mr_scanner_id",
sub_or_group_id="niiri:subject_id",
mr_protocol=q_graph.qname(NLX_FMRI_PROTOCOL)),
"ErrorModel":
dict(error_model_id="niiri:error_model_id",
noise_distribution="obo:STATO_0000227",
variance_homo="true",
variance_spatial="nidm:NIDM_0000073",
dependence="obo:STATO_0000357",
dependence_spatial="nidm:NIDM_0000074"),
"ModelParametersEstimation":
dict(model_pe_id="niiri:model_parameters_estimation_id",
label="Model Parameters Estimation",
est_method=STATO_GLS_STR,
est_method_comment=STATO_GLS_LABEL,
design_matrix_id="niiri:design_matrix_id",
data_matrix_id="niiri:data_id",
error_model_id="niiri:error_model_id",
software_id="niiri:software_id"),
"ParameterEstimateMap-1":
dict(
beta_map_id="niiri:beta_map_id_1",
label="Parameter estimate 1",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
location="ParameterEstimate_001.nii.gz",
filename="ParameterEstimate_001.nii.gz",
sha="4c755c0ae6088f8001e0458f89e51fea0e2719b5dc747fed6f617ae12ad5c\
6a643e1afcb886bcabaaac7911f5e69086c1bd084af9f75dae75913d44a783151f6",
param_est_id="niiri:model_parameters_estimation_id"),
"ParameterEstimateMap-2":
dict(
beta_map_id="niiri:beta_map_id_2",
label="Parameter estimate 2",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="b6146d013976c471fe43a083a56b8852c39a13e0566b2d04e172275bd2fc7\
b7ffb0c0ae99fac11337d3c27f131c4a00e92f5df15d32723148639a3cc9ffd7c1f",
location="ParameterEstimate_002.nii.gz",
filename="ParameterEstimate_002.nii.gz",
param_est_id="niiri:model_parameters_estimation_id"),
"ParameterEstimateMap-3":
dict(
beta_map_id="niiri:beta_map_id_3",
label="Parameter estimate 3",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="f5dd8123b389fe755086f7ad3becb5b79f39d70cf0095b08ed8c3e5cb7179\
42711264528f08fa99e58aaaf24e03581c64567864110518247d95031ef3fe2e761",
location="ParameterEstimate_003.nii.gz",
filename="ParameterEstimate_003.nii.gz",
param_est_id="niiri:model_parameters_estimation_id"),
"ParameterEstimateMap-4":
dict(
beta_map_id="niiri:beta_map_id_4",
label="Parameter estimate 4",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="aca2503769bfb6ee3801bc50c2e033755cd9844d13ee78a38aa23140ad558\
b5c6f0517c4748f84acac27cf6608222553003f418097c18f254312b49b5522b831",
location="ParameterEstimate_004.nii.gz",
filename="ParameterEstimate_004.nii.gz",
param_est_id="niiri:model_parameters_estimation_id"),
"CoordinateSpace":
dict(coordinate_space_id="niiri:coordinate_space_id_1",
label="Coordinate space",
voxel_to_world_mapping="[[ -3.5, 0, 0, 108.5], \
[ 0, 3.5, 0, -108.5], [ 0, 0, 3.5, -52.5], [ 0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3.5, 3.5, 3.5 ]",
coord_system="nidm:NIDM_0000077",
number_of_dim="3",
dimensions="[ 64, 64, 42 ]"),
"ResidualMeanSquaresMap":
dict(
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
label="Residual Mean Squares Map",
location="ResidualMeanSquares.nii.gz",
filename="ResidualMeanSquares.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="1327a300eb1e20d42c67abb3c49a47b80ecabfebd13d0ba0aca0560e8bf43\
891f0e35a958c1afa84e041f62cf0038f58b4ab71f68b0b50d4153210aeed74f4ff",
param_est_id="niiri:model_parameters_estimation_id"),
"MaskMap_Analysis":
dict( # Analysis mask
mask_id="niiri:mask_id_1",
label="Mask",
location="Mask.nii.gz",
filename="Mask.nii.gz",
user_defined="false",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="cc1a96a6111e5107eb08487e38e6d7f8164b9d1d3f1fc10948bdbcfaea642\
fe9bfae278c7fc372b65cac7232ea58fd8fb5914014e7b9a5d6200592b12b2a728b",
generated_by_act_id="niiri:model_parameters_estimation_id",
used_by_act_id="niiri:contrast_estimation_id_1"),
"ContrastWeights":
dict(contrast_id="niiri:contrast_id_1",
label="Contrast Weights: Generation",
value="[1, 0, 0, 0]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="Generation"),
"ContrastEstimation":
dict(contrast_estimation_id="niiri:contrast_estimation_id_1",
label="Contrast estimation: Generation",
software_id="niiri:software_id",
mask_id="niiri:mask_id_1",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id_1",
param_est_map="niiri:beta_map_id_1"),
"ContrastMap":
dict(
contrast_map_id="niiri:contrast_map_id_1",
label="Contrast Map: Generation",
location="Contrast.nii.gz",
format="image/nifti",
filename="Contrast.nii.gz",
contrast_name="Generation",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="4c755c0ae6088f8001e0458f89e51fea0e2719b5dc747fed6f617ae12ad5c\
6a643e1afcb886bcabaaac7911f5e69086c1bd084af9f75dae75913d44a783151f6",
contrast_est_id="niiri:contrast_estimation_id_1"),
"ContrastStandardErrorMap":
dict(
contrast_standard_error_map_id="niiri:contrast_standard_error_map\
_id_1",
label="Contrast Standard Error Map",
location="ContrastStandardError.nii.gz",
format="image/nifti",
filename="ContrastStandardError.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="8529f3ff9f10da8f332ced9d579990321475c1498b56d79ede560ba2eccf6\
d68718757dc7af78eb1e86617a41e6c9f55161f756d184e2b0fb06c3d419dc99856",
contrast_est_id="niiri:contrast_estimation_id_1"),
"DerivedMap-ContrastVariance":
dict(
derived_from_map_id="niiri:d4de4b20b2d408cd8d825ac0edb6030a",
derived_map_type="nidm:NIDM_0000135",
filename="varcope1.nii.gz",
format="image/nifti",
sha="7d183bbacc0b99cd1db84174d32445457f532bca9f774fdcc53bc1d0faa5e\
7d250a1abf03864bd90b30f96f5a7516e0056104a729a565019b0f254a8a7bced1e",
map_id="niiri:contrast_standard_error_map_id_1"),
"StatisticMap":
dict(
statistic_map_id="niiri:statistic_map_id_1",
label="T-Statistic Map: Generation",
location="TStatistic.nii.gz",
format="image/nifti",
filename="TStatistic.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="Generation",
error_dof="102",
effect_dof="1",
sha="b6286d36e678c23622b5b0486f0efb5b274f9a5e2a3ee6aceb6a0338f7745\
fb8a4d8f72b8af22c4ffb40c860bfb65940c87b03a7336cdf1a665f9cb07a5c2527",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id_1"),
"StatisticMap-Z":
dict(
statistic_map_id="niiri:z_statistic_map_id_1",
label="Z-Statistic Map: Generation",
location="ZStatistic.nii.gz",
format="image/nifti",
filename="ZStatistic.nii.gz",
statistic_type=STATO_ZSTATISTIC_STR,
stat_type_comment=STATO_ZSTATISTIC_LABEL,
contrast_name="Generation",
effect_dof="1",
error_dof="INF",
sha="3a68a4e5963766af86d22a871a4dbca9568a46441a567855b3a84dbd47ea0\
1acea11ed77b37ce85078a219adaa92264296a4548c1ba39b11ff028e8fefd95d03",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id_1"),
"HeightThreshold":
dict(
height_threshold_id="niiri:height_threshold_id",
thresh_type=OBO_STATISTIC_QNAME,
label="Height Threshold: Z>2.3",
value="2.3",
),
"ExtentThreshold":
dict(
extent_threshold_id="niiri:extent_threshold_id",
label="Extent Threshold: p<0.05 (FWE)",
thresh_type=OBO_P_VALUE_FWER_QNAME,
value="0.05",
),
"PeakDefinitionCriteria":
dict(peak_definition_criteria_id="niiri:peak_definition_criteria_id_1",
label="Peak Definition Criteria",
min_dist_peaks="0.0"),
"ClusterDefinitionCriteria":
dict(cluster_definition_criteria_id="niiri:cluster_definition_criteria\
_id_1",
label="Cluster Connectivity Criterion: 26",
connectivity="nidm:NIDM_0000129"),
"Inference":
dict(inference_id="niiri:inference_id_1",
label="Inference: Generation",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id="niiri:z_statistic_map_id_1",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
peak_def_id="niiri:peak_definition_criteria_id_1",
cluster_def_id="niiri:cluster_definition_criteria_id_1",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"),
"FSL_ExcursionSetMap":
dict(
id="niiri:excursion_set_map_id_1",
label="Excursion Set Map",
location="ExcursionSet.nii.gz",
format="image/nifti",
filename="ExcursionSet.nii.gz",
cluster_label_map_id="niiri:cluster_label_map_id",
png_id="niiri:excursion_set_png_id_1",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="c74e3c47e4308f27423a195c7c3e70b64b8fd362d612a2543da76bced67f6\
66949b70272033ab3d4b7d0bbbfe22b7da13d56d25521664be0c96454fd180ee4cc",
inference_id="niiri:inference_id_1"),
"Image":
dict(image_id="niiri:excursion_set_png_id_1",
location="ExcursionSet.png",
filename="ExcursionSet.png",
format="image/png"),
"FSL_SupraThresholdCluster-1":
dict(cluster_id="niiri:supra_threshold_cluster_0001",
label="Supra-Threshold Cluster 0001",
cluster_size_in_voxels="81",
cluster_label_id="1",
cluster_size_in_resels="23.1209189500945",
p_value_fwe="0.00894",
excursion_set_id="niiri:excursion_set_map_id_1"),
"FSL_ClusterCenterOfGravity-1":
dict(center_of_gravity_id="niiri:center_of_gravity_1",
label="Center of gravity 1",
location="niiri:COG_coordinate_0001",
cluster_id="niiri:supra_threshold_cluster_0001"),
"FSL_Coordinate-COG1":
dict(
coordinate_id="niiri:COG_coordinate_0001",
label="Coordinate 0001",
coord="[ -4.39, 28.6, 55.9 ]",
coord_in_vox="[ 32.3, 39.2, 31.0 ]",
),
"FSL_SupraThresholdCluster-2":
dict(cluster_id="niiri:supra_threshold_cluster_0002",
label="Supra-Threshold Cluster 0002",
cluster_size_in_voxels="117",
cluster_label_id="2",
cluster_size_in_resels="19.4128470430038",
p_value_fwe="0.000621",
excursion_set_id="niiri:excursion_set_map_id_1"),
"FSL_ClusterCenterOfGravity-2":
dict(center_of_gravity_id="niiri:center_of_gravity_2",
label="Center of gravity 2",
location="niiri:COG_coordinate_0002",
cluster_id="niiri:supra_threshold_cluster_0002"),
"FSL_Coordinate-COG2":
dict(
coordinate_id="niiri:COG_coordinate_0002",
label="Coordinate 0002",
coord="[ -56.4, -41.4, 16.5 ]",
coord_in_vox="[ 47.1, 19.2, 19.7 ]",
),
"FSL_SupraThresholdCluster-3":
dict(cluster_id="niiri:supra_threshold_cluster_0003 ",
label="Supra-Threshold Cluster 0003",
cluster_size_in_voxels="499",
cluster_label_id="3",
cluster_size_in_resels="19.4128470430038",
p_value_fwe="1.26e-12",
excursion_set_id="niiri:excursion_set_map_id_1"),
"FSL_ClusterCenterOfGravity-3 ":
dict(center_of_gravity_id="niiri:center_of_gravity_3 ",
label="Center of gravity 3",
location="niiri:COG_coordinate_0003 ",
cluster_id="niiri:supra_threshold_cluster_0003 "),
"FSL_Coordinate-COG3 ":
dict(
coordinate_id="niiri:COG_coordinate_0003 ",
label="Coordinate 0003",
coord="[-43.5, 32.6, 31.1]",
coord_in_vox="[ 43.4, 40.3, 23.9 ]",
),
"FSL_SupraThresholdCluster-4":
dict(cluster_id="niiri:supra_threshold_cluster_0004 ",
label="Supra-Threshold Cluster 0004",
cluster_size_in_voxels="1203",
cluster_label_id="4",
p_value_fwe="8.02e-24",
excursion_set_id="niiri:excursion_set_map_id_1"),
"FSL_ClusterCenterOfGravity-4 ":
dict(center_of_gravity_id="niiri:center_of_gravity_4",
label="Center of gravity 4",
location="niiri:COG_coordinate_0004 ",
cluster_id="niiri:supra_threshold_cluster_0004 "),
"FSL_Coordinate-COG4 ":
dict(
coordinate_id="niiri:COG_coordinate_0004 ",
label="Coordinate 0004",
coord="[-10.5, -56.9, -3.41]",
coord_in_vox="[ 34.0, 14.7, 14.0 ]",
),
"Peak-M4-1":
dict(peak_id="niiri:peak_0004_1",
label="Peak 4_01",
p_uncorr="3.51932e-09",
location="niiri:coordinate_0004_1",
equiv_z="5.79",
cluster_id="niiri:supra_threshold_cluster_0004"),
"FSL_Coordinate-4-1":
dict(
coordinate_id="niiri:coordinate_0004_1",
label="Coordinate 4_01",
coord="[ -35.0, -49.0, -7.0 ]",
coord_in_vox="[ 41, 17, 13 ]",
),
"Peak-4-2":
dict(peak_id="niiri:peak_0004_2",
label="Peak 4_02",
p_uncorr="9.01048e-09",
location="niiri:coordinate_0004_2",
equiv_z="5.63",
cluster_id="niiri:supra_threshold_cluster_0004"),
"FSL_Coordinate-4-2":
dict(
coordinate_id="niiri:coordinate_0004_2",
label="Coordinate 4_02",
coord="[-38.5, -35.0, -10.5]",
coord_in_vox="[ 42, 21, 12 ]",
),
"Peak-4-3":
dict(peak_id="niiri:peak_0004_3",
label="Peak 4_03",
p_uncorr="9.54787e-09",
location="niiri:coordinate_0004_3",
equiv_z="5.62",
cluster_id="niiri:supra_threshold_cluster_0004"),
"FSL_Coordinate-4-3":
dict(
coordinate_id="niiri:coordinate_0004_3",
label="Coordinate 4_03",
coord="[ 10.5, -84.0, 3.5]",
coord_in_vox="[ 28, 7, 16 ]",
),
"Peak-4-4":
dict(peak_id="niiri:peak_0004_4",
label="Peak 4_04",
p_uncorr="1.01163e-08",
location="niiri:coordinate_0004_4",
equiv_z="5.61",
cluster_id="niiri:supra_threshold_cluster_0004"),
"FSL_Coordinate-4-4":
dict(coordinate_id="niiri:coordinate_0004_4",
label="Coordinate 4_04",
coord="[-49.0, -56.0, -3.5]",
coord_in_vox="[ 45, 15, 14 ]"),
"Peak-4-5":
dict(peak_id="niiri:peak_0004_5",
label="Peak 4_05",
p_uncorr="1.07176e-08",
location="niiri:coordinate_0004_5",
equiv_z="5.6",
cluster_id="niiri:supra_threshold_cluster_0004"),
"FSL_Coordinate-4-5":
dict(coordinate_id="niiri:coordinate_0004_5",
label="Coordinate 4_05",
coord="[-28.0, -63.0, -10.5]",
coord_in_vox="[ 39, 13, 12 ]"),
"Peak-4-6":
dict(peak_id="niiri:peak_0004_6",
label="Peak 4_06",
p_uncorr="1.34887e-08",
location="niiri:coordinate_0004_6",
equiv_z="5.56",
cluster_id="niiri:supra_threshold_cluster_0004"),
"FSL_Coordinate-4-6":
dict(coordinate_id="niiri:coordinate_0004_6",
label="Coordinate 4_06",
coord="[-3.5, -73.5, 3.5]",
coord_in_vox="[ 32, 10, 16 ]"),
"Peak-M3-1":
dict(peak_id="niiri:peak_0003_1",
label="Peak 3_01",
p_uncorr="1.01163e-08",
location="niiri:coordinate_0003_1",
equiv_z="5.61",
cluster_id="niiri:supra_threshold_cluster_0003"),
"FSL_Coordinate-3-1":
dict(coordinate_id="niiri:coordinate_0003_1",
label="Coordinate 3_01",
coord="[-35.0, 35.0, 35.0]",
coord_in_vox="[ 41, 41, 25 ]"),
"Peak-3-2":
dict(peak_id="niiri:peak_0003_2",
label="Peak 3_02",
p_uncorr="1.52768e-07",
location="niiri:coordinate_0003_2",
equiv_z="5.12",
cluster_id="niiri:supra_threshold_cluster_0003"),
"FSL_Coordinate-3-2":
dict(coordinate_id="niiri:coordinate_0003_2",
label="Coordinate 3_02",
coord="[-42.0, 35.0, 17.5]",
coord_in_vox="[ 43, 41, 20 ]"),
"Peak-3-3":
dict(peak_id="niiri:peak_0003_3",
label="Peak 3_03",
p_uncorr="1.82833e-06",
location="niiri:coordinate_0003_3",
equiv_z="4.63",
cluster_id="niiri:supra_threshold_cluster_0003"),
"FSL_Coordinate-3-3":
dict(coordinate_id="niiri:coordinate_0003_3",
label="Coordinate 3_03",
coord="[-59.5, 21.0, 21.0]",
coord_in_vox="[ 48, 37, 21 ]"),
"Peak-3-4":
dict(peak_id="niiri:peak_0003_4",
label="Peak 3_04",
p_uncorr="9.77365e-06",
location="niiri:coordinate_0003_4",
equiv_z="4.27",
cluster_id="niiri:supra_threshold_cluster_0003"),
"FSL_Coordinate-3-4":
dict(coordinate_id="niiri:coordinate_0003_4",
label="Coordinate 3_04",
coord="[-52.5, 49.0, 24.5]",
coord_in_vox="[ 46, 45, 22 ]"),
"Peak-3-5":
dict(peak_id="niiri:peak_0003_5",
label="Peak 3_05",
p_uncorr="1.22151e-05",
location="niiri:coordinate_0003_5",
equiv_z="4.22",
cluster_id="niiri:supra_threshold_cluster_0003"),
"FSL_Coordinate-3-5":
dict(coordinate_id="niiri:coordinate_0003_5",
label="Coordinate 3_05",
coord="[-31.5, 21.0, 45.5]",
coord_in_vox="[ 40, 37, 28 ]"),
"Peak-3-6":
dict(peak_id="niiri:peak_0003_6",
label="Peak 3_06",
p_uncorr="1.89436e-05",
location="niiri:coordinate_0003_6",
equiv_z="4.12",
cluster_id="niiri:supra_threshold_cluster_0003"),
"FSL_Coordinate-3-6":
dict(coordinate_id="niiri:coordinate_0003_6",
label="Coordinate 3_06",
coord="[-49.0, 38.5, 35.0]",
coord_in_vox="[ 45, 42, 25 ]"),
"Peak-M2-1":
dict(peak_id="niiri:peak_0002_1",
label="Peak 2_01",
p_uncorr="1.74205e-06",
location="niiri:coordinate_0002_1",
equiv_z="4.64",
cluster_id="niiri:supra_threshold_cluster_0002"),
"FSL_Coordinate-2-1":
dict(coordinate_id="niiri:coordinate_0002_1",
label="Coordinate 2_01",
coord="[-56.0, -45.5, 10.5]",
coord_in_vox="[ 47, 18, 18 ]"),
"Peak-2-2":
dict(peak_id="niiri:peak_0002_2",
label="Peak 2_02",
p_uncorr="4.71165e-06",
location="niiri:coordinate_0002_2",
equiv_z="4.43",
cluster_id="niiri:supra_threshold_cluster_0002"),
"FSL_Coordinate-2-2":
dict(coordinate_id="niiri:coordinate_0002_2",
label="Coordinate 2_02",
coord="[-56.0, -38.5, 24.5]",
coord_in_vox="[ 47, 20, 22 ]"),
"Peak-M1-1":
dict(peak_id="niiri:peak_0001_1",
label="Peak 1_01",
p_uncorr="2.01334e-06",
location="niiri:coordinate_0001_1",
equiv_z="4.61",
cluster_id="niiri:supra_threshold_cluster_0001"),
"FSL_Coordinate-1-1":
dict(coordinate_id="niiri:coordinate_0001_1",
label="Coordinate 1_01",
coord="[-7.0, 24.5, 56.0]",
coord_in_vox="[ 33, 38, 31 ]"),
"Peak-1-2":
dict(peak_id="niiri:peak_0001_2",
label="Peak 1_02",
p_uncorr="0.000788846",
location="niiri:coordinate_0001_2",
equiv_z="3.16",
cluster_id="niiri:supra_threshold_cluster_0001"),
"FSL_Coordinate-1-2":
dict(coordinate_id="niiri:coordinate_0001_2",
label="Coordinate 1_02",
coord="[-7.0, 42.0, 45.5]",
coord_in_vox="[ 33, 43, 28 ]"),
"Peak-1-3":
dict(peak_id="niiri:peak_0001_3",
label="Peak 1_03",
p_uncorr="0.00122277",
location="niiri:coordinate_0001_3",
equiv_z="3.03",
cluster_id="niiri:supra_threshold_cluster_0001"),
"FSL_Coordinate-1-3":
dict(coordinate_id="niiri:coordinate_0001_3",
label="Coordinate 1_03",
coord="[-17.5, 28.0, 52.5]",
coord_in_vox="[ 36, 39, 30 ]"),
"Peak-1-4":
dict(peak_id="niiri:peak_0001_4",
label="Peak 1_04",
p_uncorr="0.00554262",
location="niiri:coordinate_0001_4",
equiv_z="2.54",
cluster_id="niiri:supra_threshold_cluster_0001"),
"FSL_Coordinate-1-4":
dict(coordinate_id="niiri:coordinate_0001_4",
label="Coordinate 1_04",
coord="[-7.0, 52.5, 42.0]",
coord_in_vox="[ 33, 46, 27 ]"),
"FSL_SearchSpaceMaskMap":
dict(
search_space_id="niiri:search_space_mask_id",
location="SearchSpaceMask.nii.gz",
filename="SearchSpaceMask.nii.gz",
label="Search Space Mask Map",
user_defined="false",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
search_vol_voxels="45203",
search_vol_units="1.93808e+06",
search_vol_resels="3753.84",
resel_size="12.0418",
noise_roughness="0.384676",
random_field_station="true",
sha="cc1a96a6111e5107eb08487e38e6d7f8164b9d1d3f1fc10948bdbcfaea642\
fe9bfae278c7fc372b65cac7232ea58fd8fb5914014e7b9a5d6200592b12b2a728b",
inference_id="niiri:inference_id_1",
noise_fwhm_in_voxels="[2.38803, 2.43263, 2.07288]",
noise_fwhm_in_units="[8.35811, 8.5142, 7.2551]"),
"NIDMBundle":
dict(bundle_id="niiri:fsl_results_id",
label="NIDM-Results",
object_model="nidm:NIDM_0000027",
version="1.3.0",
time="2014-05-19T10:30:00.000+01:00",
export_id="niiri:export_id"),
"FSL_Software":
dict(software_id="niiri:software_id",
software_type="scr:SCR_002823",
label="FSL",
version="5.0.x",
feat_version="6.00"),
"GrandMeanMap":
dict(
grand_mean_map_id="niiri:grand_mean_map_id",
label="Grand Mean Map",
location="GrandMean.nii.gz",
filename="GrandMean.nii.gz",
format="image/nifti",
masked_median="9597.36",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="7a2703cea740e27a5170fb19e4a09b5e815e4b7e477bc75958404d675aa40\
8f53f747892a2ef4472f933cf5f12cd21cea99d5f5e551938081636fb6d4049473e",
model_pe_id="niiri:model_parameters_estimation_id"),
"ExporterSoftware":
dict(software_id="niiri:exporter_id",
software_type="nidm:NIDM_0000167",
label="nidmfsl",
version="0.2.0"),
"Export":
dict(export_id="niiri:export_id",
label="NIDM-Results export",
exporter_id="niiri:exporter_id")
}
NIDM_FSL_DIR = os.path.join(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'fsl',
"example001")
ttl_file = os.path.join(NIDM_FSL_DIR, 'fsl_nidm.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def main():
nidm_classes = {
"DesignMatrix_1stLevel": dict(
design_matrix_id='niiri:design_matrix_id',
label="Design Matrix",
location="DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id",
regressors='[\\\"Sn(1) active*bf(1)\\\", \\\"Sn(1) constant\\\"]',
hrf_basis="spm:SPM_0000004",
drift_model="niiri:drift_model_id"),
"SPM_DriftModel": dict(
id="niiri:drift_model_id",
label="SPM's DCT Drift Model",
cut_off="128"
),
"Image-DesignMatrix": dict(
image_id="niiri:design_matrix_png_id",
location="DesignMatrix.png",
filename="DesignMatrix.png",
format="image/png"
),
"Data": dict(
data_id='niiri:data_id',
label="Data",
scaling="true",
target=100
),
"ErrorModel": dict(
error_model_id="niiri:error_model_id",
noise_distribution="obo:STATO_0000227",
variance_homo="true",
variance_spatial="nidm:NIDM_0000073",
dependence="obo:STATO_0000357",
dependence_spatial="nidm:NIDM_0000072"
),
"ModelParametersEstimation": dict(
model_pe_id="niiri:model_pe_id",
label="Model parameters estimation",
est_method=STATO_GLS_STR,
est_method_comment=STATO_GLS_LABEL,
design_matrix_id="niiri:design_matrix_id",
data_matrix_id="niiri:data_id",
error_model_id="niiri:error_model_id",
software_id="niiri:software_id"
),
"ParameterEstimateMap-1": dict(
beta_map_id="niiri:beta_map_id_1",
label="Beta Map 1",
coordinate_space_id="niiri:coordinate_space_id_1",
param_est_id="niiri:model_pe_id"),
"DerivedMap-PE1": dict(
derived_from_map_id="niiri:beta_map_id_1_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0001.nii",
format="image/nifti",
sha="fab2573099693215bac756bc796fbc983524473dec5c1b2d66fb83694c174\
12731df7f574094cb6c4a77994af7be11ed9aa545090fbe8ec6565a5c3c3dae8f0f",
map_id="niiri:beta_map_id_1"
),
"ParameterEstimateMap-2": dict(
beta_map_id="niiri:beta_map_id_2",
label="Beta Map 2",
coordinate_space_id="niiri:coordinate_space_id_1",
param_est_id="niiri:model_pe_id"),
"CoordinateSpace-1": dict(
coordinate_space_id="niiri:coordinate_space_id_1",
label="Coordinate space 1",
voxel_to_world_mapping="[[-3, 0, 0, 78],[0, 3, 0, -112],[0, 0, 3, \
-70],[0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000051",
number_of_dim="3",
dimensions="[ 53, 63, 52 ]"),
"ResidualMeanSquaresMap": dict(
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
label="Residual Mean Squares Map",
location="ResidualMeanSquares.nii.gz",
filename="ResidualMeanSquares.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="84cd0e608b8763307a1166b88761291e552838d85b58334a69a286060f648\
9a3b0929a940c3ccac883803455118787ea32e0bb5a6d236a5d6e9e8b6a9f918a6b",
param_est_id="niiri:model_pe_id"),
"DerivedMap-RMSMap": dict(
derived_from_map_id="niiri:residual_mean_squares_map_id_der",
derived_map_type="nidm:NIDM_0000066",
filename="ResMS.nii",
format="image/nifti",
sha="1635e0ae420cac1b5989fbc753b95f504dd957ff2986367fc4cd13ff35c44\
b4ee60994a9cdcab93a7d247fc5a8decb7578fa4c553b0ac905af8c7041db9b4acd",
map_id="niiri:residual_mean_squares_map_id"
),
"MaskMap_Analysis": dict( # The "analysis mask"
mask_id="niiri:mask_id_1",
label="Mask",
location="Mask.nii.gz",
user_defined="false",
filename="Mask.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="932fd9f0d55e9822748f4a9b35a0a7f0fe442f3e061e2eda48c2617a2938d\
f50ea84deca8de0725641a0105b712a80a0c8931df9bdf3bef788b1041379d00875",
generated_by_act_id="niiri:model_pe_id",
used_by_act_id="niiri:contrast_estimation_id"),
"DerivedMap-Mask2": dict( # The "analysis mask" (derived)
derived_from_map_id="niiri:mask_id_1_der",
derived_map_type="nidm:NIDM_0000054",
filename="mask.nii",
format="image/nifti",
sha="fbc254cab29db5532feccce554ec9d3c845197eca9013ec9f0efd5d8d56e3\
aa008ccee4038fb3651d30447fa0f316938b07c3ad961b623458dcd9b46968a8e11",
map_id="niiri:mask_id_1"
),
"ContrastWeights": dict(
contrast_id="niiri:contrast_id",
label="Contrast: passive listening > rest",
value="[1, 0]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="passive listening > rest"
),
"ContrastEstimation": dict(
contrast_estimation_id="niiri:contrast_estimation_id",
label="Contrast estimation",
software_id="niiri:software_id",
mask_id="niiri:mask_id_1",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id",
param_est_map="niiri:beta_map_id_1"
),
"ContrastEstUsedParamEst-Con1PE2": dict(
contrast_estimation_id="niiri:contrast_estimation_id",
param_est_map="niiri:beta_map_id_2"
),
"ContrastMap": dict(
contrast_map_id="niiri:contrast_map_id",
label="Contrast Map: passive listening > rest",
location="Contrast.nii.gz",
format="image/nifti",
filename="Contrast.nii.gz",
contrast_name="passive listening > rest",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="f0720b732aaf19c2ec42d0469f8308beb3aa978baf65c7dce6476a0d8e5b2\
f38c4fa9609f045a536678440feebce9a047e3bd6d59fdb8fb64baae058690bbda2",
contrast_est_id="niiri:contrast_estimation_id"),
"ContrastStandardErrorMap": dict(
contrast_standard_error_map_id="niiri:contrast_standard_error_map_\
id",
label="Contrast Standard Error Map",
location="ContrastStandardError.nii.gz",
format="image/nifti",
filename="ContrastStandardError.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="f4e3616579fe8b0812469409b1501e391bb17ca6e364f37d622b37fa9014c\
f1dd89befece07e73cf5bca5b3116f55ac4496751ca990db85e8377001a4be941b2",
contrast_est_id="niiri:contrast_estimation_id"),
"StatisticMap_T": dict(
statistic_map_id="niiri:statistic_map_id",
label="Statistic Map: passive listening > rest",
location="TStatistic.nii.gz",
format="image/nifti",
filename="TStatistic.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="passive listening > rest",
error_dof="84.0",
effect_dof="1",
sha="799e9bbf8c15b35c0098bca468846bf2cd895a3366382b5ceaa953f1e9e57\
6955341a7c86e13e6fe9359da4ff1496a609f55ce9ecff8da2e461365372f2506d6",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id"),
"DerivedMap-StatMap": dict(
derived_from_map_id="niiri:statistic_map_id_der",
derived_map_type="nidm:NIDM_0000076",
filename="spmT_0001.nii",
format="image/nifti",
sha="55951f31f0ede7e88eca5cd4793df3f630aba21bc90fb81e3695db060c7d\
4c0b0ccf0b51fd8958c32ea3253d3122e9b31a54262bf910f8b5b646054ceb9a5825",
map_id="niiri:statistic_map_id"
),
"HeightThreshold_equivThresh_equivThresh2": dict(
height_threshold_id="niiri:height_threshold_id",
thresh_type=OBO_P_VALUE_FWER_QNAME,
label="Height Threshold: p<0.05 (FWE)",
value="0.0499999999999976",
equiv_thresh="niiri:height_threshold_id_2",
equiv_thresh2="niiri:height_threshold_id_3"
),
"HeightThreshold-2": dict(
height_threshold_id="niiri:height_threshold_id_2",
thresh_type=OBO_STATISTIC_QNAME,
label="Height Threshold",
value="4.85241745689539"
),
"HeightThreshold-3": dict(
height_threshold_id="niiri:height_threshold_id_3",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
label="Height Threshold",
value="2.7772578456986e-06",
),
"ExtentThresholdStat_equivThresh_equivThresh2_clusterSizeResels": dict(
extent_threshold_id="niiri:extent_threshold_id",
label="Extent Threshold: k>=0",
cluster_size_vox="0",
cluster_size_resels="0",
equiv_thresh="niiri:extent_threshold_id_2",
equiv_thresh2="niiri:extent_threshold_id_3"
),
"ExtentThreshold-2": dict(
extent_threshold_id="niiri:extent_threshold_id_2",
label="Extent Threshold",
thresh_type=OBO_P_VALUE_FWER_QNAME,
value="1",
),
"ExtentThreshold-3": dict(
extent_threshold_id="niiri:extent_threshold_id_3",
label="Extent Threshold",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
value="1",
),
"PeakDefinitionCriteria_MaxPeaks": dict(
peak_definition_criteria_id="niiri:peak_definition_criteria_id",
label="Peak Definition Criteria",
max_num_peaks="3",
min_dist_peaks="8.0"
),
"ClusterDefinitionCriteria": dict(
cluster_definition_criteria_id="niiri:cluster_definition_criteria\
_id",
label="Cluster Connectivity Criterion: 18",
connectivity="nidm:NIDM_0000128"
),
"Inference": dict(
inference_id="niiri:inference_id",
label="Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id="niiri:statistic_map_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
Inference_mask_id="niiri:sub_volume_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"
),
"ExcursionSetMap": dict(
id="niiri:excursion_set_map_id",
label="Excursion Set Map",
location="ExcursionSet.nii.gz",
format="image/nifti",
filename="ExcursionSet.nii.gz",
cluster_label_map_id="niiri:cluster_label_map_id",
max_intensity_projection_id="niiri:maximum_intensity_projection\
_id",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="d96b82761c299a66978893cab6034f3f8aed25d0a135636b0ffe79f4cf11b\
ecce86ba261f7aeb43717f5d0e47ad0b14cfb0402786251e3f2c507890c83b27652",
num_of_clusters="5",
p_value="2.83510681598e-09",
inference_id="niiri:inference_id"
),
"SupraThresholdCluster-1": dict(
cluster_id="niiri:supra_threshold_cluster_0001",
label="Supra-Threshold Cluster: 0001",
cluster_size_in_voxels="839",
cluster_label_id="1",
cluster_size_in_resels="6.31265696809113",
p_value_unc="3.55896824480477e-19",
p_value_fwe="0",
p_value_fdr="1.77948412240239e-18",
excursion_set_id="niiri:excursion_set_map_id"
),
"SupraThresholdCluster-2": dict(
cluster_id="niiri:supra_threshold_cluster_0002",
label="Supra-Threshold Cluster: 0002",
cluster_size_in_voxels="695",
cluster_label_id="2",
cluster_size_in_resels="5.22919736927692",
p_value_unc="5.34280282632073e-17",
p_value_fwe="0",
p_value_fdr="1.33570070658018e-16",
excursion_set_id="niiri:excursion_set_map_id"
),
"SupraThresholdCluster-3": dict(
cluster_id="niiri:supra_threshold_cluster_0003",
label="Supra-Threshold Cluster: 0003",
cluster_size_in_voxels="37",
cluster_label_id="3",
cluster_size_in_resels="0.278388924695318",
p_value_unc="0.00497953247554004",
p_value_fwe="0.000255384009130943",
p_value_fdr="0.00829922079256674",
excursion_set_id="niiri:excursion_set_map_id"
),
"SupraThresholdCluster-4": dict(
cluster_id="niiri:supra_threshold_cluster_0004",
label="Supra-Threshold Cluster: 0004",
cluster_size_in_voxels="29",
cluster_label_id="4",
cluster_size_in_resels="0.218196724761195",
p_value_unc="0.0110257032104773",
p_value_fwe="0.000565384750377596",
p_value_fdr="0.0137821290130967",
excursion_set_id="niiri:excursion_set_map_id"
),
"SupraThresholdCluster-5": dict(
cluster_id="niiri:supra_threshold_cluster_0005",
label="Supra-Threshold Cluster: 0005",
cluster_size_in_voxels="12",
cluster_label_id="5",
cluster_size_in_resels="0.0902882999011843",
p_value_unc="0.0818393184514307",
p_value_fwe="0.00418900977248904",
p_value_fdr="0.0818393184514307",
excursion_set_id="niiri:excursion_set_map_id"
),
"Peak_ValueP-1": dict(
peak_id="niiri:peak_0001",
label="Peak: 0001",
location="niiri:coordinate_0001",
value="17.5207633972168",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="1.19156591713838e-11",
cluster_id="niiri:supra_threshold_cluster_0001"
),
"Coordinate-1": dict(
coordinate_id="niiri:coordinate_0001",
label="Coordinate: 0001",
coord="[ -60, -25, 11 ]"
),
"Peak_ValueP-2": dict(
peak_id="niiri:peak_0002",
label="Peak: 0002",
location="niiri:coordinate_0002",
value="13.0321407318",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="1.19156591714e-11",
cluster_id="niiri:supra_threshold_cluster_0001"
),
"Coordinate-2": dict(
coordinate_id="niiri:coordinate_0002",
label="Coordinate: 0002",
coord="[ -42, -31, 11 ]"
),
"Peak_ValueP-3": dict(
peak_id="niiri:peak_0003",
label="Peak: 0003",
location="niiri:coordinate_0003",
value="10.2856016159058",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="7.69451169446711e-12",
p_value_fdr="6.84121260274992e-10",
cluster_id="niiri:supra_threshold_cluster_0001"
),
"Coordinate-3": dict(
coordinate_id="niiri:coordinate_0003",
label="Coordinate: 0003",
coord="[ -66, -31, -1 ]"
),
"Peak_ValueP-4": dict(
peak_id="niiri:peak_0004",
label="Peak: 0004",
location="niiri:coordinate_0004",
value="13.5425577163696",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="1.19156591713838e-11",
cluster_id="niiri:supra_threshold_cluster_0002"
),
"Coordinate-4": dict(
coordinate_id="niiri:coordinate_0004",
label="Coordinate: 0004",
coord="[ 63, -13, -4 ]"
),
"Peak_ValueP-5": dict(
peak_id="niiri:peak_0005",
label="Peak: 0005",
location="niiri:coordinate_0005",
value="12.4728717803955",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="1.19156591713838e-11",
cluster_id="niiri:supra_threshold_cluster_0002"
),
"Coordinate-5": dict(
coordinate_id="niiri:coordinate_0005",
label="Coordinate: 0005",
coord="[ 60, -22, 11 ]"
),
"Peak_ValueP-6": dict(
peak_id="niiri:peak_0006",
label="Peak: 0006",
location="niiri:coordinate_0006",
value="9.72103404998779",
equiv_z="INF",
p_uncorr="1.22124532708767e-15",
p_value_fwe="6.9250605250204e-11",
p_value_fdr="6.52169693024352e-09",
cluster_id="niiri:supra_threshold_cluster_0002"
),
"Coordinate-6": dict(
coordinate_id="niiri:coordinate_0006",
label="Coordinate: 0006",
coord="[ 57, -40, 5 ]"
),
"Peak_ValueP-7": dict(
peak_id="niiri:peak_0007",
label="Peak: 0007",
location="niiri:coordinate_0007",
value="6.55745935440063",
equiv_z="5.87574033699266",
p_uncorr="2.10478867668229e-09",
p_value_fwe="9.17574302586877e-05",
p_value_fdr="0.00257605396646668",
cluster_id="niiri:supra_threshold_cluster_0003"
),
"Coordinate-7": dict(
coordinate_id="niiri:coordinate_0007",
label="Coordinate: 0007",
coord="[ 36, -28, -13 ]"
),
"Peak_ValueP-8": dict(
peak_id="niiri:peak_0008",
label="Peak: 0008",
location="niiri:coordinate_0008",
value="6.19558477401733",
equiv_z="5.60645028016544",
p_uncorr="1.0325913235576e-08",
p_value_fwe="0.000382453907303626",
p_value_fdr="0.00949154522981781",
cluster_id="niiri:supra_threshold_cluster_0004"
),
"Coordinate-8": dict(
coordinate_id="niiri:coordinate_0008",
label="Coordinate: 0008",
coord="[ -33, -31, -16 ]"
),
"Peak_ValueP-9": dict(
peak_id="niiri:peak_0009",
label="Peak: 0009",
location="niiri:coordinate_0009",
value="5.27320194244385",
equiv_z="4.88682085490477",
p_uncorr="5.12386299833523e-07",
p_value_fwe="0.0119099090973821",
p_value_fdr="0.251554254717758",
cluster_id="niiri:supra_threshold_cluster_0005"
),
"Coordinate-9": dict(
coordinate_id="niiri:coordinate_0009",
label="Coordinate: 0009",
coord="[ 45, -40, 32 ]"
),
"SearchSpaceMaskMap": dict( # The "search space"
search_space_id="niiri:search_space_mask_id",
location="SearchSpaceMask.nii.gz",
filename="SearchSpaceMask.nii.gz",
label="Search Space Mask Map",
format="image/nifti",
user_defined="false",
coordinate_space_id="niiri:coordinate_space_id_1",
expected_num_voxels="4.02834655908613",
expected_num_clusters="0.0512932943875478",
height_critical_fwe05="4.85241745689539",
height_critical_fdr05="5.7639536857605",
smallest_size_fwe05="12",
smallest_size_fdr05="29",
search_vol_voxels="69306",
search_vol_units="1871262",
resel_size="132.907586178202",
search_vol_resels="467.07642343881",
search_vol_resels_geom="[7, 42.96312274763, 269.40914815306, \
467.07642343881]",
noise_fwhm_in_voxels="[ 5.41278985910694, 5.43638957240286, \
4.51666658877481 ]",
noise_fwhm_in_units="[ 16.2383695773208, 16.3091687172086, \
13.5499997663244 ]",
random_field_station="true",
sha="932fd9f0d55e9822748f4a9b35a0a7f0fe442f3e061e2eda48c2617a2938\
df50ea84deca8de0725641a0105b712a80a0c8931df9bdf3bef788b1041379d00875",
inference_id="niiri:inference_id"
),
"DerivedMap": dict(
derived_from_map_id="niiri:contrast_map_id_der",
derived_map_type="nidm:NIDM_0000002",
filename="con_0001.nii",
format="image/nifti",
sha="277dd1da13d391c33c172fb8c71060008cc66e173de6362eb857b0055b41e\
9bae57911f7ec4b45659905103b1139ebf3da0c2d04cf105bbce0cdc3004b643c22",
map_id="niiri:contrast_map_id"
),
"DerivedMap-2": dict(
derived_from_map_id="niiri:beta_map_id_2_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0002.nii",
format="image/nifti",
sha="3f72b788762d9ab2c7ddb5e4d446872694ee42fc8897fe5317b54efb7924f\
784da6499065db897a49595d8763d1893ad65ad102b0c88f2e72e2d028173343008",
map_id="niiri:beta_map_id_2"
),
"NIDMBundle": dict(
bundle_id="niiri:spm_results_id",
label="NIDM-Results",
object_model="nidm:NIDM_0000027",
version="1.1.0",
time="2014-05-19T10:30:00.000+01:00",
export_id="niiri:export_id"
),
"SPM_ReselsPerVoxelMap": dict(
resels_per_voxel_map_id="niiri:resels_per_voxel_map_id",
label="Resels per Voxel Map",
location="ReselsPerVoxel.nii.gz",
filename="ReselsPerVoxel.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="2025dc6c33708b80708c2eba3215fb1149df236fb558a8e8f8f6cf34595fb\
54734fe5e436db3e192a424d99699dd7feb2f4a9020ceae8e7bcbd881b17825256a",
model_pe_id="niiri:model_pe_id"
),
"SPM_InferenceUsedRPVMap": dict(
inference_id="niiri:inference_id",
resels_per_voxel_map_id="niiri:resels_per_voxel_map_id"
),
"DerivedMap-RPVMap": dict(
derived_from_map_id="niiri:resels_per_voxel_map_id_der",
derived_map_type="nidm:NIDM_0000144",
filename="RPV.nii",
format="image/nifti",
sha="963283cdde607c40e4640c27453867bd0d70133b6d61482933862487c0f4a\
5acdb2e338a12a2605ee044b1aa47b5717f0c520b90ed3c49b5227f0483bd48512d",
map_id="niiri:resels_per_voxel_map_id"
),
"ClusterLabelsMap": dict(
cluster_label_map_id="niiri:cluster_label_map_id",
location="ClusterLabels.nii.gz",
filename="ClusterLabels.nii.gz",
format="image/nifti"
),
"SPM_Software": dict(
software_id="niiri:software_id",
software_type="nlx:nif-0000-00343",
label="SPM",
version="12.12.1"
),
"Image": dict(
image_id="niiri:maximum_intensity_projection_id",
location="MaximumIntensityProjection.png",
filename="MaximumIntensityProjection.png",
format="image/png"
),
"GrandMeanMap": dict(
grand_mean_map_id="niiri:grand_mean_map_id",
label="Grand Mean Map",
location="GrandMean.nii.gz",
filename="GrandMean.nii.gz",
format="image/nifti",
masked_median="132.008995056152",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="4d3528031bce4a9c1b994b8124e6e0eddb9df90b49c84787652ed94df8c14\
c04ec92100a2d8ea86a8df24ba44617aca7457ddcb2f42253fc17e33296a1aea1cb",
model_pe_id="niiri:model_pe_id"
),
"ExporterSoftware": dict(
software_id="niiri:exporter_id",
software_type="nidm:NIDM_0000168",
label="spm_results_nidm",
version="12b.5858"
),
"Export": dict(
export_id="niiri:export_id",
label="NIDM-Results export",
exporter_id="niiri:exporter_id"
)
}
NIDM_SPM_DIR = os.path.join(os.path.dirname(
os.path.dirname(os.path.abspath(__file__))), 'spm', "example001")
ttl_file = os.path.join(NIDM_SPM_DIR, 'example001_spm_results.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def main():
nidm_classes = {
"DesignMatrix":
dict(design_matrix_id='niiri:design_matrix_id',
label="Design Matrix",
location="file:///path/to/DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id"),
"Image-DesignMatrix":
dict(image_id="niiri:design_matrix_png_id",
location="file:///path/to/DesignMatrix.png",
filename="DesignMatrix.png",
format="image/png"),
"Data":
dict(data_id='niiri:data_id', label="Data", scaling="true",
target=100),
"ErrorModel":
dict(error_model_id="niiri:error_model_id",
noise_distribution="nidm:NIDM_0000032",
variance_homo="true",
variance_spatial="nidm:NIDM_0000073",
dependence="nidm:NIDM_0000048",
dependence_spatial="nidm:NIDM_0000073"),
"ModelParametersEstimation":
dict(model_pe_id="niiri:model_pe_id",
label="Model parameters estimation",
est_method=STATO_OLS_STR,
est_method_comment=STATO_OLS_LABEL,
design_matrix_id="niiri:design_matrix_id",
data_matrix_id="niiri:data_id",
error_model_id="niiri:error_model_id",
software_id="niiri:software_id"),
"ParameterEstimateMap_Location-1":
dict(beta_map_id="niiri:beta_map_id_1",
label="Beta Map 1",
location="file:///path/to/ParameterEstimate_0001.nii.gz",
filename="ParameterEstimate_0001.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_pe_id"),
"DerivedMap-PE1":
dict(derived_from_map_id="niiri:beta_map_id_1_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0001.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:beta_map_id_1"),
"ParameterEstimateMap_Location-2":
dict(beta_map_id="niiri:beta_map_id_2",
label="Beta Map 2",
location="file:///path/to/ParameterEstimate_0002.nii.gz",
filename="ParameterEstimate_0002.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_pe_id"),
"DerivedMap-PE2":
dict(derived_from_map_id="niiri:beta_map_id_2_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0002.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:beta_map_id_2"),
"ParameterEstimateMap_Location-3":
dict(beta_map_id="niiri:beta_map_id_3",
label="Beta Map 3",
location="file:///path/to/ParameterEstimate_0003.nii.gz",
filename="ParameterEstimate_0003.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_pe_id"),
"DerivedMap-PE3":
dict(derived_from_map_id="niiri:beta_map_id_3_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0003.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:beta_map_id_3"),
"CoordinateSpace-1":
dict(
coordinate_space_id="niiri:coordinate_space_id_1",
label="Coordinate space 1",
voxel_to_world_mapping="[[-3, 0, 0, 78],[0, 3, 0, -112],[0, 0, 3, \
-50],[0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000051",
number_of_dim="3",
dimensions="[ 53, 63, 46 ]"),
"ResidualMeanSquaresMap":
dict(residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
label="Residual Mean Squares Map",
location="file:///path/to/ResidualMeanSquares.nii.gz",
filename="ResidualMeanSquares.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_pe_id"),
"MaskMap_Analysis":
dict( # The analysis mask
mask_id="niiri:mask_id_1",
label="Mask",
location="file:///path/to/Mask.nii.gz",
filename="Mask.nii.gz",
user_defined="false",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
generated_by_act_id="niiri:model_pe_id",
# fixme: also used by niiri:contrast_estimation_id_2
used_by_act_id="niiri:contrast_estimation_id"),
"ContrastWeights":
dict(contrast_id="niiri:contrast_id",
label="Contrast: listening > reading",
value="[1, -1, 0, 0]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > reading"),
"ContrastWeights-2":
dict(contrast_id="niiri:contrast_id_2",
label="Contrast: motor",
value="[ 0, 0, 1 ]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="motor"),
"ContrastEstimation":
dict(contrast_estimation_id="niiri:contrast_estimation_id",
label="Contrast estimation 1",
software_id="niiri:software_id",
mask_id="niiri:mask_id_1",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id",
param_est_map="niiri:beta_map_id_1"),
"ContrastEstUsedParamEst-Con1PE2":
dict(contrast_estimation_id="niiri:contrast_estimation_id",
param_est_map="niiri:beta_map_id_2"),
"ContrastEstimation-2":
dict(contrast_estimation_id="niiri:contrast_estimation_id_2",
label="Contrast estimation 2",
software_id="niiri:software_id",
mask_id="niiri:mask_id_1",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id_2",
param_est_map="niiri:beta_map_id_3"),
"ContrastEstUsedParamEst-Con2PE3":
dict(contrast_estimation_id="niiri:contrast_estimation_id_2",
param_est_map="niiri:beta_map_id_3"),
"ContrastMap":
dict(contrast_map_id="niiri:contrast_map_id",
label="Contrast Map: listening > reading",
location="file:///path/to/Contrast_0001.nii.gz",
format="image/nifti",
filename="Contrast_0001.nii.gz",
contrast_name="listening > reading",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
contrast_est_id="niiri:contrast_estimation_id"),
"ContrastMap-2":
dict(contrast_map_id="niiri:contrast_map_id_2",
label="Contrast Map: motor",
location="file:///path/to/Contrast_0002.nii.gz",
format="image/nifti",
filename="Contrast_0002.nii.gz",
contrast_name="motor",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
contrast_est_id="niiri:contrast_estimation_id_2"),
"DerivedMap-ContrastMap-2":
dict(derived_from_map_id="niiri:contrast_map_id_2_der",
derived_map_type="nidm:NIDM_0000002",
filename="con_0002.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:contrast_map_id_2"),
"ContrastStandardErrorMap":
dict(
contrast_standard_error_map_id="niiri:contrast_standard_error_map_\
id",
label="Contrast 1 Standard Error Map",
location="file:///path/to/ContrastStandardError_0001.nii.gz",
format="image/nifti",
filename="ContrastStandardError_0001.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
contrast_est_id="niiri:contrast_estimation_id"),
"ContrastStandardErrorMap-2":
dict(
contrast_standard_error_map_id="niiri:contrast_standard_error_map_\
id_2",
label="Contrast 2 Standard Error Map",
location="file:///path/to/ContrastStandardError_0002.nii.gz",
format="image/nifti",
filename="ContrastStandardError_0002.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
contrast_est_id="niiri:contrast_estimation_id_2"),
"StatisticMap_T":
dict(statistic_map_id="niiri:statistic_map_id",
label="Statistic Map: listening > reading",
location="file:///path/to/TStatistic_0001.nii.gz",
format="image/nifti",
filename="TStatistic_0001.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > reading",
error_dof="72.9999999990787",
effect_dof="1",
sha="e43b6e01b0463fe7d40782137867a...",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id"),
"DerivedMap-StatMap":
dict(derived_from_map_id="niiri:statistic_map_id_der",
derived_map_type="nidm:NIDM_0000076",
filename="spmT_0001.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:statistic_map_id"),
"StatisticMap_T-2":
dict(statistic_map_id="niiri:statistic_map_id_2",
label="Statistic Map: motor",
location="file:///path/to/TStatistic_0002.nii.gz",
format="image/nifti",
filename="TStatistic_0002.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="motor",
error_dof="72.9999999990787",
effect_dof="1",
sha="e43b6e01b0463fe7d40782137867a...",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id_2"),
"DerivedMap-StatMap-2":
dict(derived_from_map_id="niiri:statistic_map_id_2_der",
derived_map_type="nidm:NIDM_0000076",
filename="spmT_0002.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:statistic_map_id_2"),
"HeightThreshold_equivThresh_equivThresh2":
dict(height_threshold_id="niiri:height_threshold_id",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
label="Height Threshold: p<7.62276079258051e-07 (unc)",
value="7.62276079258051e-07",
equiv_thresh="niiri:height_threshold_id_2",
equiv_thresh2="niiri:height_threshold_id_3"),
"HeightThreshold-2":
dict(height_threshold_id="niiri:height_threshold_id_2",
thresh_type=OBO_STATISTIC_QNAME,
label="Height Threshold",
value="5.23529984739211"),
"HeightThreshold-3":
dict(
height_threshold_id="niiri:height_threshold_id_3",
thresh_type=OBO_P_VALUE_FWER_QNAME,
label="Height Threshold",
value="0.05",
),
"ExtentThresholdStat_equivThresh_equivThresh2_clusterSizeResels":
dict(extent_threshold_id="niiri:extent_threshold_id",
label="Extent Threshold: k>=10",
cluster_size_vox="10",
cluster_size_resels="3.3",
equiv_thresh="niiri:height_threshold_id_2",
equiv_thresh2="niiri:height_threshold_id_3"),
"ExtentThreshold-2":
dict(
extent_threshold_id="niiri:extent_threshold_id_2",
label="Extent Threshold",
thresh_type=OBO_P_VALUE_FWER_QNAME,
value="1",
),
"ExtentThreshold-3":
dict(
extent_threshold_id="niiri:extent_threshold_id_3",
label="Extent Threshold",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
value="1",
),
"DisplayMaskMap":
dict(display_map_id="niiri:display_map_id",
label="Display Mask Map",
user_defined="true",
location="file:///path/to/DisplayMask.nii.gz",
filename="DisplayMask.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a..."),
"PeakDefinitionCriteria_MaxPeaks":
dict(peak_definition_criteria_id="niiri:peak_definition_criteria_id",
label="Peak Definition Criteria",
max_num_peaks="3",
min_dist_peaks="8.0"),
"ClusterDefinitionCriteria":
dict(
cluster_definition_criteria_id="niiri:cluster_definition_criteria_\
id",
label="Cluster Connectivity Criterion: 18",
connectivity="nidm:NIDM_0000128"),
"ConjunctionInference":
dict(conj_inference_id="niiri:inference_id",
label="Conjunction Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id_1="niiri:statistic_map_id",
stat_map_id_2="niiri:statistic_map_id_2",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
display_mask_id="niiri:display_map_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"),
"DerivedMap-Contrast":
dict(derived_from_map_id="niiri:contrast_map_id_der",
derived_map_type="nidm:NIDM_0000002",
filename="con_0001.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:contrast_map_id"),
"NIDMBundle":
dict(bundle_id="niiri:spm_results_id",
label="NIDM-Results",
object_model="nidm:NIDM_0000027",
version="1.1.0",
time="2014-05-19T10:30:00.000+01:00"),
"SPM_ReselsPerVoxelMap":
dict(resels_per_voxel_map_id="niiri:resels_per_voxel_map_id",
label="Resels per Voxel Map",
location="file:///path/to/ReselsPerVoxel.nii.gz",
filename="ReselsPerVoxel.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
model_pe_id="niiri:model_pe_id"),
"SPM_InferenceUsedRPVMap":
dict(inference_id="niiri:inference_id",
resels_per_voxel_map_id="niiri:resels_per_voxel_map_id"),
"DerivedMap-RPV":
dict(derived_from_map_id="niiri:resels_per_voxel_map_id_der",
derived_map_type="nidm:NIDM_0000144",
filename="RPV.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:resels_per_voxel_map_id"),
"SPM_Software":
dict(software_id="niiri:software_id",
software_type="nlx:nif-0000-00343",
label="SPM",
version="12b.5853"),
"GrandMeanMap":
dict(grand_mean_map_id="niiri:grand_mean_map_id",
label="Grand Mean Map",
location="file:///path/to/GrandMean.nii.gz",
filename="GrandMean.nii.gz",
format="image/nifti",
masked_median="115",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
model_pe_id="niiri:model_pe_id")
}
NIDM_SPM_DIR = os.path.join(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'spm',
"example003")
ttl_file = os.path.join(NIDM_SPM_DIR, 'spm_results_conjunction.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def main():
nidm_classes = {
"DesignMatrix": dict(
design_matrix_id='niiri:design_matrix_id',
label="Design Matrix",
location="file:///path/to/DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id"),
"Image-DesignMatrix": dict(
image_id="niiri:design_matrix_png_id",
location="file://./DesignMatrix.png",
filename="DesignMatrix.png",
format="image/png"
),
"Data": dict(
data_id='niiri:data_id',
label="Data",
scaling="true",
target=100
),
"ErrorModel": dict(
error_model_id="niiri:error_model_id",
noise_distribution="nidm:NIDM_0000032",
variance_homo="true",
variance_spatial="nidm:NIDM_0000073",
dependence="nidm:NIDM_0000048",
dependence_spatial="nidm:NIDM_0000073"
),
"ModelParametersEstimation": dict(
model_pe_id="niiri:model_pe_id",
label="Model parameters estimation",
est_method=STATO_OLS_STR,
est_method_comment=STATO_OLS_LABEL,
software_id="niiri:software_id",
design_matrix_id="niiri:design_matrix_id",
data_matrix_id="niiri:data_id",
error_model_id="niiri:error_model_id"
),
"ParameterEstimateMap": dict(
beta_map_id="niiri:beta_map_id_1",
label="Beta Map 1",
location="file:///path/to/ParameterEstimate_0001.nii.gz",
filename="ParameterEstimate_0001.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_pe_id"),
"ResidualMeanSquaresMap": dict(
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
label="Residual Mean Squares Map",
location="file:///path/to/ResidualMeanSquares.nii.gz",
filename="ResidualMeanSquares.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_pe_id"),
"MaskMap": dict(
mask_id="niiri:mask_id_2",
user_defined="false",
label="Mask",
location="file:///path/to/Mask.nii.gz",
filename="Mask.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
used_by_act_id="niiri:model_pe_id"),
"ContrastWeights": dict(
contrast_id="niiri:contrast_id",
label="Contrast: Listening > Rest",
value="[ 1, 0, 0 ]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > rest"),
"ContrastEstimation": dict(
contrast_estimation_id="niiri:contrast_estimation_id",
label="Contrast estimation",
software_id="niiri:software_id",
mask_id="niiri:mask_id_2",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id",
param_est_map="niiri:beta_map_id_1"),
"ContrastMap": dict(
contrast_map_id="niiri:contrast_map_id",
label="Contrast Map: listening > rest",
location="file:///path/to/Contrast.nii.gz",
format="image/nifti",
filename="Contrast.nii.gz",
contrast_name="listening > rest",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
contrast_est_id="niiri:contrast_estimation_id"),
"ContrastStandardErrorMap": dict(
contrast_standard_error_map_id="niiri:contrast_standard_error_map_\
id",
label="Contrast Standard Error Map",
location="file:///path/to/ContrastStandardError.nii.gz",
format="image/nifti",
filename="ContrastStandardError.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
contrast_est_id="niiri:contrast_estimation_id"),
"StatisticMap_T": dict(
statistic_map_id="niiri:statistic_map_id",
label="Statistic Map: listening > rest",
location="file:///path/to/TStatistic.nii.gz",
format="image/nifti",
filename="TStatistic.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > rest",
error_dof="72.9999999990787",
effect_dof="1",
sha="e43b6e01b0463fe7d40782137867a...",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id"),
"HeightThreshold_equivThresh-FWER": dict(
height_threshold_id="niiri:height_threshold_fwer_id",
label="Height Threshold: p<0.05 (FWER-corrected)",
value="0.05",
thresh_type=OBO_P_VALUE_FWER_QNAME,
equiv_thresh="niiri:height_threshold_stat_id"
),
"HeightThreshold-Stat": dict(
height_threshold_id="niiri:height_threshold_stat_id",
label="Height Threshold: Z<0.0000000672357409",
value="0.0000000672357409",
thresh_type=OBO_STATISTIC_QNAME,
),
"HeightThreshold-FDR": dict(
height_threshold_id="niiri:height_threshold_fdr_id",
label="Height Threshold: p<0.05 (FDR-corrected)",
value="0.05",
thresh_type=OBO_Q_VALUE_FDR_QNAME
),
"HeightThreshold-Unc": dict(
height_threshold_id="niiri:height_threshold_unc_id",
label="Height Threshold: p<0.001 (uncorrected)",
value="0.001",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME
),
"ExtentThresholdStat_clusterSizeResels": dict(
extent_threshold_id="niiri:extent_threshold_stat_id",
label="Extent Threshold: k>=0",
cluster_size_vox="0",
cluster_size_resels="0",
),
"ExtentThreshold_equivThresh-FWER": dict(
extent_threshold_id="niiri:extent_threshold_fwer_id",
thresh_type=OBO_P_VALUE_FWER_QNAME,
label="Extent Threshold: p<0.05 (FWER-corrected)",
value="0.05",
equiv_thresh="niiri:extent_threshold_stat_id"
),
"ExtentThreshold-FDR": dict(
extent_threshold_id="niiri:extent_threshold_fdr_id",
thresh_type=OBO_Q_VALUE_FDR_QNAME,
label="Extent Threshold: p<0.05 (FDR-corrected)",
value="0.05"
),
"ExtentThreshold-Unc": dict(
extent_threshold_id="niiri:extent_threshold_unc_id",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
label="Extent Threshold: p<0.001 (uncorrected)",
value="0.001"
),
"SPM_ReselsPerVoxelMap": dict(
resels_per_voxel_map_id="niiri:resels_per_voxel_map_id",
label="Resels per Voxel Map",
location="file:///path/to/ReselsPerVoxel.nii.gz",
filename="ReselsPerVoxel.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
model_pe_id="niiri:model_pe_id"
),
"ClusterLabelsMap": dict(
cluster_label_map_id="niiri:cluster_label_map_id",
location="file:///path/to/ClusterLabels.nii.gz",
filename="ClusterLabels.nii.gz",
format="image/nifti"
),
"DisplayMaskMap": dict(
display_map_id="niiri:display_map_id",
label="Display Mask Map",
location="file:///path/to/DisplayMask.nii.gz",
filename="DisplayMask.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_2",
sha="e43b6e01b0463fe7d40782137867a..."
),
"PeakDefinitionCriteria_MaxPeaks": dict(
peak_definition_criteria_id="niiri:peak_definition_criteria_id",
label="Peak Definition Criteria",
max_num_peaks="3",
min_dist_peaks="8.0"
),
"ClusterDefinitionCriteria": dict(
cluster_definition_criteria_id="niiri:cluster_definition_criteria_\
id",
label="Cluster Connectivity Criterion: 18",
connectivity="nidm:NIDM_0000128"
),
"Inference": dict(
inference_id="niiri:inference_id",
label="Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id="niiri:statistic_map_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
inference_mask_id="niiri:mask_id_3",
display_mask_id="niiri:display_map_id",
mask_id="niiri:mask_id",
software_id="niiri:software_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id"
),
"ExcursionSetMap": dict(
id="niiri:excursion_set_map_id",
label="Excursion Set Map",
location="file:///path/to/ExcursionSet.nii.gz",
format="image/nifti",
filename="ExcursionSet.nii.gz",
cluster_label_map_id="niiri:cluster_label_map_id",
max_intensity_projection_id="niiri:maximum_intensity_projection_\
id",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
num_of_clusters="8",
p_value="8.95949980872501e-14",
inference_id="niiri:inference_id"
),
"SignificantCluster": dict(
cluster_id="niiri:significant_cluster_0001",
label="Significant Cluster 0001",
cluster_size_in_voxels="530",
cluster_label_id="1",
cluster_size_in_resels="23.1209189500945",
p_value_unc="9.56276736481136e-52",
p_value_fwe="0",
p_value_fdr="7.65021389184909e-51",
excursion_set_id="niiri:excursion_set_map_id"
),
"Peak_ValueP": dict(
peak_id="niiri:peak_0001",
label="Peak 0001",
location="niiri:coordinate_0001",
value="13.9346199035645",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="6.3705194444993e-11",
cluster_id="niiri:significant_cluster_0001"
),
"Coordinate": dict(
coordinate_id="niiri:coordinate_0001",
label="Coordinate: 0001",
coord="[ -60, -28, 13 ]"
),
"SearchSpaceMaskMap": dict(
search_space_id="niiri:search_space_mask_id",
location="file:///path/to/SearchSpaceMask.nii.gz",
filename="SearchSpaceMask.nii.gz",
label="Search Space Mask Map",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_2",
expected_num_voxels="0.553331387916112",
expected_num_clusters="0.0889172687960151",
height_critical_fwe05="5.23529984739211",
height_critical_fdr05="6.22537899017334",
smallest_size_fwe05="1",
smallest_size_fdr05="3",
search_vol_voxels="65593",
search_vol_units="1771011",
resel_size="22.9229643140043",
search_vol_resels="2552.68032521656",
search_vol_resels_geom="[3, 72.3216126440484, 850.716735116472, \
2552.68032521656]",
noise_fwhm_in_voxels="[ 2.95881189165801, 2.96628446669584, \
2.61180425626264 ]",
noise_fwhm_in_units="[ 8.87643567497404, 8.89885340008753, \
7.83541276878791 ]",
random_field_station="false",
sha="e43b6e01b0463fe7d40782137867a...",
inference_id="niiri:inference_id"
),
"FSL_ClusterCenterOfGravity": dict(
center_of_gravity_id="niiri:center_of_gravity_1",
location="niiri:coordinate_0001",
label="Center of gravity",
cluster_id="niiri:significant_cluster_0001",
),
"CoordinateSpace": dict(
coordinate_space_id="niiri:coordinate_space_id_1",
label="Coordinate space 1",
voxel_to_world_mapping="[[-3, 0, 0, 78],[0, 3, 0, -112],\
[0, 0, 3, -50],[0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000051",
number_of_dim="3",
dimensions="[ 53, 63, 46 ]"),
"Image": dict(
image_id="niiri:maximum_intensity_projection_id",
location="file:///path/to/MaximumIntensityProjection.png",
filename="MaximumIntensityProjection.png",
format="image/png"
),
"GrandMeanMap": dict(
grand_mean_map_id="niiri:grand_mean_map_id",
label="Grand Mean Map",
location="file:///path/to/GrandMean.nii.gz",
filename="GrandMean.nii.gz",
format="image/nifti",
masked_median="115",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
model_pe_id="niiri:model_pe_id"
),
"SPM_DriftModel": dict(
id="niiri:drift_model_id",
label="SPM's DCT Drift Model",
cut_off="128"
),
"FSL_DriftModel": dict(
id="niiri:drift_model_id",
label="FSL's Gaussian Running Line Drift Model",
cut_off="2"
)
}
NIDM_TERMS_DIR = os.path.join(os.path.dirname(
os.path.dirname(os.path.abspath(__file__))), 'terms')
EX_DIR = os.path.join(NIDM_TERMS_DIR, 'examples')
example = ExampleFromTemplate(nidm_classes, EX_DIR, True)
example.create_example()
def main():
nidm_classes = {
"DesignMatrix_1stLevel":
dict(design_matrix_id='niiri:design_matrix_id',
label="Design Matrix",
location="file://./DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id",
regressors="[\\\"Gen\\\", \\\"Gen*temporal_derivative\\\""
", \\\"Shad\\\", \\\"Shad*temporal_derivative\\\"]",
design="nidm:" + str(NIDM_EVENT_RELATED_DESIGN).split("#")[1],
hrf_basis="fsl:FSL_0000001",
drift_model="niiri:drift_model_id"),
"FSL_DriftModel":
dict(id="niiri:drift_model_id",
label="FSL's Gaussian Running Line Drift Model",
cut_off="1908"),
"Image_fileName-DesignMatrix":
dict(image_id="niiri:design_matrix_png_id",
location="file://./DesignMatrix.png",
filename="DesignMatrix.png",
filename_2="design.png",
format="image/png"),
"Data":
dict(data_id='niiri:data_id',
label="Data",
scaling="true",
target="10000"),
"ErrorModel":
dict(error_model_id="niiri:error_model_id",
noise_distribution="nidm:NIDM_0000032",
variance_homo="true",
variance_spatial="nidm:NIDM_0000073",
dependence="obo:STATO_0000357",
dependence_spatial="nidm:NIDM_0000074"),
"ModelParametersEstimation":
dict(model_pe_id="niiri:model_parameters_estimation_id",
label="Model Parameters Estimation",
est_method=STATO_GLS_STR,
est_method_comment=STATO_GLS_LABEL,
design_matrix_id="niiri:design_matrix_id",
data_matrix_id="niiri:data_id",
error_model_id="niiri:error_model_id",
software_id="niiri:software_id"),
"FSL_ParameterEstimateMapNoLocation-1":
dict(beta_map_id="niiri:beta_map_id_1",
label="Parameter estimate 1",
filename="pe1.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_parameters_estimation_id"),
"FSL_ParameterEstimateMapNoLocation-2":
dict(beta_map_id="niiri:beta_map_id_2",
label="Parameter estimate 2",
filename="pe2.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_parameters_estimation_id"),
"FSL_ParameterEstimateMapNoLocation-3":
dict(beta_map_id="niiri:beta_map_id_3",
label="Parameter estimate 3",
filename="pe3.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_parameters_estimation_id"),
"FSL_ParameterEstimateMapNoLocation-4":
dict(beta_map_id="niiri:beta_map_id_4",
label="Parameter estimate 4",
filename="pe4.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_parameters_estimation_id"),
"CoordinateSpace":
dict(coordinate_space_id="niiri:coordinate_space_id_1",
label="Coordinate space",
voxel_to_world_mapping="[[ -3.5, 0, 0, 108.5], \
[ 0, 3.5, 0, -108.5], [ 0, 0, 3.5, -52.5], [ 0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3.5, 3.5, 3.5 ]",
coord_system="nidm:NIDM_0000077",
number_of_dim="3",
dimensions="[ 64, 64, 42 ]"),
"FSL_ResidualMeanSquaresMap":
dict(
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
label="Residual Mean Squares Map",
location="file://./ResidualMeanSquares.nii.gz",
filename_1="ResidualMeanSquares.nii.gz",
filename_2="sigmasquareds.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="1327a300eb1e20d42c67abb3c49a47b80ecabfebd13d0ba0aca0560e8bf43\
891f0e35a958c1afa84e041f62cf0038f58b4ab71f68b0b50d4153210aeed74f4ff",
param_est_id="niiri:model_parameters_estimation_id"),
"MaskMap_Analysis_fileName":
dict( # Analysis mask
mask_id="niiri:mask_id_1",
label="Mask",
location="file://./Mask.nii.gz",
filename="Mask.nii.gz",
filename_2="mask.nii.gz",
user_defined="false",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="cc1a96a6111e5107eb08487e38e6d7f8164b9d1d3f1fc10948bdbcfaea642\
fe9bfae278c7fc372b65cac7232ea58fd8fb5914014e7b9a5d6200592b12b2a728b",
generated_by_act_id="niiri:model_parameters_estimation_id",
used_by_act_id="niiri:contrast_estimation_id_1"),
"ContrastWeights":
dict(contrast_id="niiri:contrast_id_1",
label="Contrast Weights: Generation",
value="[1, 0, 0, 0]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="Generation"),
"ContrastEstimation":
dict(contrast_estimation_id="niiri:contrast_estimation_id_1",
label="Contrast estimation: Generation",
software_id="niiri:software_id",
mask_id="niiri:mask_id_1",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id_1",
param_est_map="niiri:beta_map_id_1"),
"FSL_ContrastMap":
dict(
contrast_map_id="niiri:contrast_map_id_1",
label="Contrast Map: Generation",
location="file://./Contrast.nii.gz",
format="image/nifti",
filename_1="Contrast.nii.gz",
filename_2="cope1.nii.gz",
contrast_name="Generation",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="4c755c0ae6088f8001e0458f89e51fea0e2719b5dc747fed6f617ae12ad5c\
6a643e1afcb886bcabaaac7911f5e69086c1bd084af9f75dae75913d44a783151f6",
contrast_est_id="niiri:contrast_estimation_id_1"),
"ContrastStandardErrorMap":
dict(
contrast_standard_error_map_id="niiri:contrast_standard_error_map\
_id_1",
label="Contrast Standard Error Map",
location="file://./ContrastStandardError.nii.gz",
format="image/nifti",
filename="ContrastStandardError.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="8529f3ff9f10da8f332ced9d579990321475c1498b56d79ede560ba2eccf6\
d68718757dc7af78eb1e86617a41e6c9f55161f756d184e2b0fb06c3d419dc99856",
contrast_est_id="niiri:contrast_estimation_id_1"),
"DerivedMap-ContrastVariance":
dict(
derived_from_map_id="niiri:d4de4b20b2d408cd8d825ac0edb6030a",
derived_map_type="nidm:NIDM_0000135",
filename="varcope1.nii.gz",
format="image/nifti",
sha="7d183bbacc0b99cd1db84174d32445457f532bca9f774fdcc53bc1d0faa5e\
7d250a1abf03864bd90b30f96f5a7516e0056104a729a565019b0f254a8a7bced1e",
map_id="niiri:contrast_standard_error_map_id_1"),
"FSL_StatisticMap":
dict(
statistic_map_id="niiri:statistic_map_id_1",
label="Statistic Map: Generation",
location="file://./TStatistic.nii.gz",
format="image/nifti",
filename_1="TStatistic.nii.gz",
filename_2="tstat1.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="Generation",
error_dof="102",
effect_dof="1",
sha="b6286d36e678c23622b5b0486f0efb5b274f9a5e2a3ee6aceb6a0338f7745\
fb8a4d8f72b8af22c4ffb40c860bfb65940c87b03a7336cdf1a665f9cb07a5c2527",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id_1"),
"FSL_StatisticMap-Z":
dict(
statistic_map_id="niiri:z_statistic_map_id_1",
label="Z-Statistic Map: Generation",
location="file://./ZStatistic.nii.gz",
format="image/nifti",
filename_1="ZStatistic.nii.gz",
filename_2="zstat1.nii.gz",
statistic_type=STATO_ZSTATISTIC_STR,
stat_type_comment=STATO_ZSTATISTIC_LABEL,
contrast_name="Generation",
effect_dof="1",
error_dof="INF",
sha="3a68a4e5963766af86d22a871a4dbca9568a46441a567855b3a84dbd47ea0\
1acea11ed77b37ce85078a219adaa92264296a4548c1ba39b11ff028e8fefd95d03",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id_1"),
"HeightThreshold":
dict(
height_threshold_id="niiri:height_threshold_id",
thresh_type=OBO_STATISTIC_QNAME,
label="Height Threshold: Z>2.3",
value="2.3",
),
"ExtentThreshold":
dict(
extent_threshold_id="niiri:extent_threshold_id",
label="Extent Threshold: p<0.05 (FWE)",
thresh_type=OBO_P_VALUE_FWER_QNAME,
value="0.05",
),
"PeakDefinitionCriteria":
dict(peak_definition_criteria_id="niiri:peak_definition_criteria_id_1",
label="Peak Definition Criteria",
min_dist_peaks="0.0"),
"ClusterDefinitionCriteria":
dict(cluster_definition_criteria_id="niiri:cluster_definition_criteria\
_id_1",
label="Cluster Connectivity Criterion: 26",
connectivity="nidm:NIDM_0000129"),
"Inference":
dict(inference_id="niiri:inference_id_1",
label="Inference: Generation",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id="niiri:z_statistic_map_id_1",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
peak_def_id="niiri:peak_definition_criteria_id_1",
cluster_def_id="niiri:cluster_definition_criteria_id_1",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"),
"FSL_ExcursionSetMap":
dict(
id="niiri:excursion_set_map_id_1",
label="Excursion Set Map",
location="file://./ExcursionSet.nii.gz",
format="image/nifti",
filename_1="ExcursionSet.nii.gz",
filename_2="thresh_zstat1.nii.gz",
cluster_label_map_id="niiri:cluster_label_map_id",
png_id="niiri:excursion_set_png_id_1",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="c74e3c47e4308f27423a195c7c3e70b64b8fd362d612a2543da76bced67f6\
66949b70272033ab3d4b7d0bbbfe22b7da13d56d25521664be0c96454fd180ee4cc",
inference_id="niiri:inference_id_1"),
"Image":
dict(image_id="niiri:excursion_set_png_id_1",
location="file://./rendered_thresh_zstat1.png",
filename="rendered_thresh_zstat1.png",
format="image/png"),
"FSL_SignificantCluster-1":
dict(cluster_id="niiri:significant_cluster_0001",
label="Significant Cluster 0001",
cluster_size_in_voxels="81",
cluster_label_id="1",
cluster_size_in_resels="23.1209189500945",
p_value_fwe="0.00894",
excursion_set_id="niiri:excursion_set_map_id_1"),
"FSL_ClusterCenterOfGravity-1":
dict(center_of_gravity_id="niiri:center_of_gravity_1",
label="Center of gravity 1",
location="niiri:COG_coordinate_0001",
cluster_id="niiri:significant_cluster_0001"),
"FSL_Coordinate-COG1":
dict(
coordinate_id="niiri:COG_coordinate_0001",
label="Coordinate 0001",
coord="[ -5.8, 19.1, 38.5 ]",
coord_in_vox="[ 32.3, 39.2, 31.0 ]",
),
"FSL_SignificantCluster-2":
dict(cluster_id="niiri:significant_cluster_0002",
label="Significant Cluster 0002",
cluster_size_in_voxels="117",
cluster_label_id="2",
cluster_size_in_resels="19.4128470430038",
p_value_fwe="0.000621",
excursion_set_id="niiri:excursion_set_map_id_1"),
"FSL_ClusterCenterOfGravity-2":
dict(center_of_gravity_id="niiri:center_of_gravity_2",
label="Center of gravity 2",
location="niiri:COG_coordinate_0002",
cluster_id="niiri:significant_cluster_0002"),
"FSL_Coordinate-COG2":
dict(
coordinate_id="niiri:COG_coordinate_0002",
label="Coordinate 0002",
coord="[ -56.9, -57.1, 9.86 ]",
coord_in_vox="[ 47.1, 19.2, 19.7 ]",
),
"FSL_SignificantCluster-3":
dict(cluster_id="niiri:significant_cluster_0003 ",
label="Significant Cluster 0003",
cluster_size_in_voxels="499",
cluster_label_id="3",
cluster_size_in_resels="19.4128470430038",
p_value_fwe="1.26e-12",
excursion_set_id="niiri:excursion_set_map_id_1"),
"FSL_ClusterCenterOfGravity-3 ":
dict(center_of_gravity_id="niiri:center_of_gravity_3 ",
label="Center of gravity 3",
location="niiri:COG_coordinate_0003 ",
cluster_id="niiri:significant_cluster_0003 "),
"FSL_Coordinate-COG3 ":
dict(
coordinate_id="niiri:COG_coordinate_0003 ",
label="Coordinate 0003",
coord="[ -47.2, 17.3, 9.18 ]",
coord_in_vox="[ 43.4, 40.3, 23.9 ]",
),
"FSL_SignificantCluster-4":
dict(cluster_id="niiri:significant_cluster_0004 ",
label="Significant Cluster 0004",
cluster_size_in_voxels="1203",
cluster_label_id="4",
p_value_fwe="8.02e-24",
excursion_set_id="niiri:excursion_set_map_id_1"),
"FSL_ClusterCenterOfGravity-4 ":
dict(center_of_gravity_id="niiri:center_of_gravity_4",
label="Center of gravity 4",
location="niiri:COG_coordinate_0004 ",
cluster_id="niiri:significant_cluster_0004 "),
"FSL_Coordinate-COG4 ":
dict(
coordinate_id="niiri:COG_coordinate_0004 ",
label="Coordinate 0004",
coord="[ -7.38, -72.5, -8.5 ]",
coord_in_vox="[ 34.0, 14.7, 14.0 ]",
),
"Peak-M4-1":
dict(peak_id="niiri:peak_0004_1",
label="Peak 0004_1",
p_uncorr="3.51932e-09",
location="niiri:coordinate_0004_1",
equiv_z="5.79",
cluster_id="niiri:significant_cluster_0004"),
"FSL_Coordinate-4-1":
dict(
coordinate_id="niiri:coordinate_0004_1",
label="Coordinate 0004_1",
coord="[ -33.7, -66.7, -14.7 ]",
coord_in_vox="[ 41, 17, 13 ]",
),
"Peak-4-2":
dict(peak_id="niiri:peak_0004_2",
label="Peak 0004_2",
p_uncorr="9.01048e-09",
location="niiri:coordinate_0004_2",
equiv_z="5.63",
cluster_id="niiri:significant_cluster_0004"),
"FSL_Coordinate-4-2":
dict(
coordinate_id="niiri:coordinate_0004_2",
label="Coordinate 0004_2",
coord="[ -38.0, -53.9, -21.9 ]",
coord_in_vox="[ 42, 21, 12 ]",
),
"Peak-4-3":
dict(peak_id="niiri:peak_0004_3",
label="Peak 0004_3",
p_uncorr="9.54787e-09",
location="niiri:coordinate_0004_3",
equiv_z="5.62",
cluster_id="niiri:significant_cluster_0004"),
"FSL_Coordinate-4-3":
dict(
coordinate_id="niiri:coordinate_0004_3",
label="Coordinate 0004_3",
coord="[ 16.1, -96.6, 5.82 ]",
coord_in_vox="[ 28, 7, 16 ]",
),
"Peak-4-4":
dict(peak_id="niiri:peak_0004_4",
label="Peak 0004_4",
p_uncorr="1.01163e-08",
location="niiri:coordinate_0004_4",
equiv_z="5.61",
cluster_id="niiri:significant_cluster_0004"),
"FSL_Coordinate-4-4":
dict(coordinate_id="niiri:coordinate_0004_4",
label="Coordinate 0004_4",
coord="[ -48.1, -73.7, -9.24 ]",
coord_in_vox="[ 45, 15, 14 ]"),
"Peak-4-5":
dict(peak_id="niiri:peak_0004_5",
label="Peak 0004_5",
p_uncorr="1.07176e-08",
location="niiri:coordinate_0004_5",
equiv_z="5.6",
cluster_id="niiri:significant_cluster_0004"),
"FSL_Coordinate-4-5":
dict(coordinate_id="niiri:coordinate_0004_5",
label="Coordinate 0004_5",
coord="[ -25.5, -80.4, -15.3 ]",
coord_in_vox="[ 39, 13, 12 ]"),
"Peak-4-6":
dict(peak_id="niiri:peak_0004_6",
label="Peak 0004_6",
p_uncorr="1.34887e-08",
location="niiri:coordinate_0004_6",
equiv_z="5.56",
cluster_id="niiri:significant_cluster_0004"),
"FSL_Coordinate-4-6":
dict(coordinate_id="niiri:coordinate_0004_6",
label="Coordinate 0004_6",
coord="[ 0.791, -87.2, 3.23 ]",
coord_in_vox="[ 32, 10, 16 ]"),
"Peak-M3-1":
dict(peak_id="niiri:peak_0003_1",
label="Peak 0003_1",
p_uncorr="1.01163e-08",
location="niiri:coordinate_0003_1",
equiv_z="5.61",
cluster_id="niiri:significant_cluster_0003"),
"FSL_Coordinate-3-1":
dict(coordinate_id="niiri:coordinate_0003_1",
label="Coordinate 0003_1",
coord="[ -38.3, 20.7, 13.2 ]",
coord_in_vox="[ 41, 41, 25 ]"),
"Peak-3-2":
dict(peak_id="niiri:peak_0003_2",
label="Peak 0003_2",
p_uncorr="1.52768e-07",
location="niiri:coordinate_0003_2",
equiv_z="5.12",
cluster_id="niiri:significant_cluster_0003"),
"FSL_Coordinate-3-2":
dict(coordinate_id="niiri:coordinate_0003_2",
label="Coordinate 0003_2",
coord="[ -45.5, 17.8, -6.65 ]",
coord_in_vox="[ 43, 41, 20 ]"),
"Peak-3-3":
dict(peak_id="niiri:peak_0003_3",
label="Peak 0003_3",
p_uncorr="1.82833e-06",
location="niiri:coordinate_0003_3",
equiv_z="4.63",
cluster_id="niiri:significant_cluster_0003"),
"FSL_Coordinate-3-3":
dict(coordinate_id="niiri:coordinate_0003_3",
label="Coordinate 0003_3",
coord="[ -63.4, 3.78, 0.366 ]",
coord_in_vox="[ 48, 37, 21 ]"),
"Peak-3-4":
dict(peak_id="niiri:peak_0003_4",
label="Peak 0003_4",
p_uncorr="9.77365e-06",
location="niiri:coordinate_0003_4",
equiv_z="4.27",
cluster_id="niiri:significant_cluster_0003"),
"FSL_Coordinate-3-4":
dict(coordinate_id="niiri:coordinate_0003_4",
label="Coordinate 0003_4",
coord="[ -57.4, 31.8, -2.12 ]",
coord_in_vox="[ 46, 45, 22 ]"),
"Peak-3-5":
dict(peak_id="niiri:peak_0003_5",
label="Peak 0003_5",
p_uncorr="1.22151e-05",
location="niiri:coordinate_0003_5",
equiv_z="4.22",
cluster_id="niiri:significant_cluster_0003"),
"FSL_Coordinate-3-5":
dict(coordinate_id="niiri:coordinate_0003_5",
label="Coordinate 0003_5",
coord="[ -34.0, 8.84, 28.3 ]",
coord_in_vox="[ 40, 37, 28 ]"),
"Peak-3-6":
dict(peak_id="niiri:peak_0003_6",
label="Peak 0003_6",
p_uncorr="1.89436e-05",
location="niiri:coordinate_0003_6",
equiv_z="4.12",
cluster_id="niiri:significant_cluster_0003"),
"FSL_Coordinate-3-6":
dict(coordinate_id="niiri:coordinate_0003_6",
label="Coordinate 0003_6",
coord="[ -53.3, 23.3, 12.2 ]",
coord_in_vox="[ 45, 42, 25 ]"),
"Peak-M2-1":
dict(peak_id="niiri:peak_0002_1",
label="Peak 0002_1",
p_uncorr="1.74205e-06",
location="niiri:coordinate_0002_1",
equiv_z="4.64",
cluster_id="niiri:significant_cluster_0002"),
"FSL_Coordinate-2-1":
dict(coordinate_id="niiri:coordinate_0002_1",
label="Coordinate 0002_1",
coord="[ -56.2, -61.9, 4.03 ]",
coord_in_vox="[ 47, 18, 18 ]"),
"Peak-2-2":
dict(peak_id="niiri:peak_0002_2",
label="Peak 0002_2",
p_uncorr="4.71165e-06",
location="niiri:coordinate_0002_2",
equiv_z="4.43",
cluster_id="niiri:significant_cluster_0002"),
"FSL_Coordinate-2-2":
dict(coordinate_id="niiri:coordinate_0002_2",
label="Coordinate 0002_2",
coord="[ -56.7, -53.1, 18.2 ]",
coord_in_vox="[ 47, 20, 22 ]"),
"Peak-M1-1":
dict(peak_id="niiri:peak_0001_1",
label="Peak 0001_1",
p_uncorr="2.01334e-06",
location="niiri:coordinate_0001_1",
equiv_z="4.61",
cluster_id="niiri:significant_cluster_0001"),
"FSL_Coordinate-1-1":
dict(coordinate_id="niiri:coordinate_0001_1",
label="Coordinate 0001_1",
coord="[ -8.35, 15.1, 39.6 ]",
coord_in_vox="[ 33, 38, 31 ]"),
"Peak-1-2":
dict(peak_id="niiri:peak_0001_2",
label="Peak 0001_2",
p_uncorr="0.000788846",
location="niiri:coordinate_0001_2",
equiv_z="3.16",
cluster_id="niiri:significant_cluster_0001"),
"FSL_Coordinate-1-2":
dict(coordinate_id="niiri:coordinate_0001_2",
label="Coordinate 0001_2",
coord="[ -9.14, 30.5, 23.7 ]",
coord_in_vox="[ 33, 43, 28 ]"),
"Peak-1-3":
dict(peak_id="niiri:peak_0001_3",
label="Peak 0001_3",
p_uncorr="0.00122277",
location="niiri:coordinate_0001_3",
equiv_z="3.03",
cluster_id="niiri:significant_cluster_0001"),
"FSL_Coordinate-1-3":
dict(coordinate_id="niiri:coordinate_0001_3",
label="Coordinate 0001_3",
coord="[ -19.6, 17.4, 34.7 ]",
coord_in_vox="[ 36, 39, 30 ]"),
"Peak-1-4":
dict(peak_id="niiri:peak_0001_4",
label="Peak 0001_4",
p_uncorr="0.00554262",
location="niiri:coordinate_0001_4",
equiv_z="2.54",
cluster_id="niiri:significant_cluster_0001"),
"FSL_Coordinate-1-4":
dict(coordinate_id="niiri:coordinate_0001_4",
label="Coordinate 0001_4",
coord="[ -9.64, 40.1, 17.3 ]",
coord_in_vox="[ 33, 46, 27 ]"),
"FSL_SearchSpaceMaskMap":
dict(
search_space_id="niiri:search_space_mask_id",
location="file://./SearchSpaceMask.nii.gz",
filename_1="SearchSpaceMask.nii.gz",
filename_2="mask.nii.gz",
label="Search Space Mask Map",
user_defined="false",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
search_vol_voxels="45203",
search_vol_units="1.93808e+06",
search_vol_resels="3753.84",
resel_size="12.0418",
noise_roughness="0.384676",
random_field_station="true",
sha="cc1a96a6111e5107eb08487e38e6d7f8164b9d1d3f1fc10948bdbcfaea642\
fe9bfae278c7fc372b65cac7232ea58fd8fb5914014e7b9a5d6200592b12b2a728b",
inference_id="niiri:inference_id_1",
noise_fwhm_in_voxels="[2.38803, 2.43263, 2.07288]",
noise_fwhm_in_units="[8.35811, 8.5142, 7.2551]"),
"NIDMBundle":
dict(bundle_id="niiri:fsl_results_id",
label="NIDM-Results",
object_model="nidm:NIDM_0000027",
version="1.1.0",
time="2014-05-19T10:30:00.000+01:00"),
"FSL_Software":
dict(software_id="niiri:software_id",
software_type="nlx:birnlex_2067",
label="FSL",
version="5.0.x",
feat_version="6.00"),
"FSL_GrandMeanMap":
dict(
grand_mean_map_id="niiri:grand_mean_map_id",
label="Grand Mean Map",
location="file://./GrandMean.nii.gz",
filename_1="GrandMean.nii.gz",
filename_2="mean_func.nii.gz",
format="image/nifti",
masked_median="9597.36",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="7a2703cea740e27a5170fb19e4a09b5e815e4b7e477bc75958404d675aa40\
8f53f747892a2ef4472f933cf5f12cd21cea99d5f5e551938081636fb6d4049473e",
model_pe_id="niiri:model_parameters_estimation_id")
}
NIDM_FSL_DIR = os.path.join(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'fsl',
"example001")
ttl_file = os.path.join(NIDM_FSL_DIR, 'fsl_nidm.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def main():
nidm_classes = {
"NIDMBundle":
dict(comment="NIDM-Results Bundle",
bundle_id="niiri:nidm_results_id",
label="NIDM-Results",
object_model="nidm:NIDM_0000027",
version="1.3.0",
time="2014-05-19T10:30:00.000+01:00",
export_id="niiri:export_id"),
"SPM_Software":
dict(software_id="niiri:spm_software_id",
software_type="scr:SCR_007037",
label="SPM",
version="8.6225"),
"FSL_Software":
dict(software_id="niiri:software_id",
software_type="scr:SCR_002823",
label="FSL",
version="5.0.1",
feat_version="6.00"),
"ExporterSoftware-FSL":
dict(software_id="niiri:exporter_id",
software_type="nidm:NIDM_0000167",
label="nidmfsl",
version="0.2.0"),
"Export":
dict(export_id="niiri:export_id",
label="NIDM-Results export",
exporter_id="niiri:exporter_id"),
"ExporterSoftware-SPM":
dict(software_id="niiri:exporter_id",
software_type="nidm:NIDM_0000168",
label="spm_results_nidm",
version="12b.5858"),
"DesignMatrix":
dict(comment="Design Matrix: Group Level",
design_matrix_id='niiri:design_matrix_id',
label="Design Matrix",
location="DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id"),
"DesignMatrix_1stLevel":
dict(comment="Design Matrix: Subject Level",
design_matrix_id='niiri:first_level_design_matrix_id',
label="First-Level Design Matrix",
location="DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id",
hrf_basis="niiri:hrf_basis_id",
drift_model="niiri:drift_model_id",
regressors="[\\\"Sn(1) active*bf(1)\\\",\\\"Sn(1) constant\\\"]"),
"DesignMatrix_1stLevel-FIR":
dict(comment="HRF: FIR Basis Set",
design_matrix_id='niiri:first_level_design_matrix_id',
label="First-Level Design Matrix",
location="DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id",
hrf_basis=NIDM_FINITE_IMPULSE_RESPONSE_HRB,
drift_model="niiri:drift_model_id",
regressors="[\\\"Sn(1) active*bf(1)\\\",\\\"Sn(1) constant\\\"]"),
"DesignMatrix_1stLevel_HRFBasis2_HRFBasis3-InformedBasisSet":
dict(comment="HRF: SPM's Informed Basis Set",
design_matrix_id='niiri:first_level_design_matrix_id',
label="First-Level Design Matrix",
location="DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id",
hrf_basis=SPM_CANONICAL_HRF,
hrf_basis_2=SPM_TEMPORAL_DERIVATIVE,
hrf_basis_3=SPM_DISPERSION_DERIVATIVE,
drift_model="niiri:drift_model_id",
regressors="[\\\"Sn(1) active*bf(1)\\\",\\\"Sn(1) constant\\\"]"),
"Map_atLocation-nii":
dict(comment="Map: One-file Nifti (.nii)",
map_type="nidm:NIDM_0000052",
map_id="niiri:map_id",
filename='image.nii',
coordinate_space_id="niiri:coordinate_space_id",
sha="e43b6e01b0463fe7d40782137867ae43b6e01b0463fe7d40782137867a",
location="image.nii"),
"Map_atLocation_hasMapHeader-img":
dict(comment="Map: Nifti (.img)",
map_type="nidm:NIDM_0000052",
map_id="niiri:map_id",
filename='image.img',
coordinate_space_id="niiri:coordinate_space_id",
sha="e43b6e01b0463fe7d40782137867ae43b6e01b0463fe7d40782137867a",
map_header="niiri:map_header_id",
location="image.img"),
"MapHeader":
dict(comment="Map Header: Nifti header (.hdr)",
map_header_id="niiri:map_header_id",
filename='image.hdr',
sha="e43b6e01b0463fe7d40782137867ae43b6e01b0463fe7d40782137867a",
location="image.hdr"),
"Image-DesignMatrix":
dict(comment="Image: Design Matrix",
image_id="niiri:design_matrix_png_id",
location="DesignMatrix.png",
filename="DesignMatrix.png",
format="image/png"),
"Group":
dict(comment="Group: Control group with 23 subjects",
id="niiri:group_id",
label="Group: Control",
name="Control",
numsubjects="23"),
"Data_wasAttributedTo":
dict(
comment="Data",
data_id='niiri:data_id',
label="Data",
scaling="true",
target=100,
scanner_id="niiri:my_scanner_id",
sub_or_group_id="niiri:group_id",
group2_id="niiri:group2_id",
mr_protocol=q_graph.qname(NLX_FMRI_PROTOCOL),
),
"ImagingInstrument":
dict(
id="niiri:mr_scanner_id",
label="MRI Scanner",
type=q_graph.qname(NLX_MRI_SCANNER),
),
"ErrorModel-OLS":
dict(comment="Error Model: Ordinary least squares",
error_model_id="niiri:error_model_id",
noise_distribution=STATO_GAUSSIAN_DISTRIBUTION,
variance_homo="true",
variance_spatial=NIDM_SPATIALLY_LOCAL_MODEL,
dependence=NIDM_INDEPENDENT_ERROR,
dependence_spatial=NIDM_SPATIALLY_LOCAL_MODEL),
"ErrorModel-WLS":
dict(comment="Error Model: Weighted least squares",
error_model_id="niiri:error_model_id",
noise_distribution=STATO_GAUSSIAN_DISTRIBUTION,
variance_homo="false",
variance_spatial=NIDM_SPATIALLY_LOCAL_MODEL,
dependence=NIDM_INDEPENDENT_ERROR,
dependence_spatial=NIDM_SPATIALLY_LOCAL_MODEL),
"ErrorModel-SPMnonSphericity":
dict(comment="Error Model: SPM non sphericity",
error_model_id="niiri:error_model_id",
noise_distribution=STATO_GAUSSIAN_DISTRIBUTION,
variance_homo="false",
variance_spatial=NIDM_SPATIALLY_LOCAL_MODEL,
dependence=STATO_UNSTRUCTURED_COVARIANCE,
dependence_spatial=NIDM_SPATIALLY_GLOBAL_MODEL),
"ModelParametersEstimation":
dict(comment="Model Parameters Estimation",
model_pe_id="niiri:model_pe_id",
label="Model parameters estimation",
est_method=STATO_OLS_STR,
est_method_comment=STATO_OLS_LABEL,
software_id="niiri:software_id",
design_matrix_id="niiri:design_matrix_id",
data_matrix_id="niiri:data_id",
error_model_id="niiri:error_model_id"),
"ParameterEstimateMap":
dict(comment="Parameter Estimate Map",
beta_map_id="niiri:beta_map_id_1",
label="Beta Map 1",
location="ParameterEstimate_001.nii.gz",
filename="ParameterEstimate_001.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_pe_id"),
"ResidualMeanSquaresMap":
dict(comment="Residual Mean Squares Map",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
label="Residual Mean Squares Map",
location="ResidualMeanSquares.nii.gz",
filename="ResidualMeanSquares.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_pe_id"),
"MaskMap":
dict(comment="Mask Map",
mask_id="niiri:mask_id_2",
user_defined="false",
label="Mask",
location="Mask.nii.gz",
filename="Mask.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
used_by_act_id="niiri:model_pe_id"),
"ContrastWeights":
dict(comment="Contrast Weights",
contrast_id="niiri:contrast_id",
label="Contrast: Listening > Rest",
value="[ 1, 0, 0 ]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > rest"),
"ContrastEstimation":
dict(comment="Contrast Estimation",
contrast_estimation_id="niiri:contrast_estimation_id",
label="Contrast estimation",
software_id="niiri:software_id",
mask_id="niiri:mask_id_2",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id",
param_est_map="niiri:beta_map_id_1"),
"ContrastMap":
dict(comment="Contrast Map",
contrast_map_id="niiri:contrast_map_id",
label="Contrast Map: listening > rest",
location="Contrast.nii.gz",
format="image/nifti",
filename="Contrast.nii.gz",
contrast_name="listening > rest",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
contrast_est_id="niiri:contrast_estimation_id"),
"ContrastStandardErrorMap":
dict(
comment="Contrast Standard Error Map",
contrast_standard_error_map_id="niiri:contrast_standard_error_map_\
id",
label="Contrast Standard Error Map",
location="ContrastStandardError.nii.gz",
format="image/nifti",
filename="ContrastStandardError.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
contrast_est_id="niiri:contrast_estimation_id"),
"StatisticMap-T":
dict(comment="Statistic Map: T",
statistic_map_id="niiri:statistic_map_id",
label="T-Statistic Map: listening > rest",
location="TStatistic.nii.gz",
format="image/nifti",
filename="TStatistic.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > rest",
error_dof="72.9999999990787",
effect_dof="1",
sha="e43b6e01b0463fe7d40782137867a",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id"),
"HeightThreshold_equivThresh-FWER":
dict(comment="Height Threshold: p<0.05 FWER",
height_threshold_id="niiri:height_threshold_fwer_id",
label="Height Threshold: p<0.05 (FWER-corrected)",
value="0.05",
thresh_type=OBO_P_VALUE_FWER_QNAME,
equiv_thresh="niiri:height_threshold_stat_id"),
"HeightThreshold-Stat":
dict(
comment="Height Threshold: Z<0.0000000672357409",
height_threshold_id="niiri:height_threshold_stat_id",
label="Height Threshold: Z<0.0000000672357409",
value="0.0000000672357409",
thresh_type=OBO_STATISTIC_QNAME,
),
"HeightThreshold-FDR":
dict(comment="Height Threshold: p<0.05 FDR",
height_threshold_id="niiri:height_threshold_fdr_id",
label="Height Threshold: p<0.05 (FDR-corrected)",
value="0.05",
thresh_type=OBO_Q_VALUE_FDR_QNAME),
"HeightThreshold-Unc":
dict(comment="Height Threshold: p<0.001 uncorrected",
height_threshold_id="niiri:height_threshold_unc_id",
label="Height Threshold: p<0.001 (uncorrected)",
value="0.001",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME),
"ExtentThresholdStat_clusterSizeResels":
dict(
comment="Extent Threshold: k>=0",
extent_threshold_id="niiri:extent_threshold_stat_id",
label="Extent Threshold: k>=0",
cluster_size_vox="0",
cluster_size_resels="0",
),
"ExtentThreshold_equivThresh-FWER":
dict(comment="Extent Threshold: p<0.05 FWER",
extent_threshold_id="niiri:extent_threshold_fwer_id",
thresh_type=OBO_P_VALUE_FWER_QNAME,
label="Extent Threshold: p<0.05 (FWER-corrected)",
value="0.05",
equiv_thresh="niiri:extent_threshold_stat_id"),
"ExtentThreshold-FDR":
dict(comment="Extent Threshold: p<0.05 FDR",
extent_threshold_id="niiri:extent_threshold_fdr_id",
thresh_type=OBO_Q_VALUE_FDR_QNAME,
label="Extent Threshold: p<0.05 (FDR-corrected)",
value="0.05"),
"ExtentThreshold-Unc":
dict(comment="Extent Threshold: p<0.001 uncorrected",
extent_threshold_id="niiri:extent_threshold_unc_id",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
label="Extent Threshold: p<0.001 (uncorrected)",
value="0.001"),
"SPM_ReselsPerVoxelMap":
dict(comment="Resels per Voxel Map",
resels_per_voxel_map_id="niiri:resels_per_voxel_map_id",
label="Resels per Voxel Map",
location="ReselsPerVoxel.nii.gz",
filename="ReselsPerVoxel.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
model_pe_id="niiri:model_pe_id"),
"ClusterLabelsMap":
dict(
comment="Cluster Labels Map",
cluster_label_map_id="niiri:cluster_label_map_id",
location="ClusterLabels.nii.gz",
filename="ClusterLabels.nii.gz",
format="image/nifti",
label="Cluster Labels Map",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="13093aae03897e2518307d000eb298f4b1439814d8d3d77c622b717423f93\
506dd5de5669513ab65c6dd74a7d27ee9df08620f546ed00575517b40e5878c2c96"),
"DisplayMaskMap":
dict(comment="Display Mask Map",
display_map_id="niiri:display_map_id",
label="Display Mask Map",
location="DisplayMask.nii.gz",
filename="DisplayMask.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_2",
sha="e43b6e01b0463fe7d40782137867a"),
"PeakDefinitionCriteria_MaxPeaks":
dict(comment="Peak Definition Criteria",
peak_definition_criteria_id="niiri:peak_definition_criteria_id",
label="Peak Definition Criteria",
max_num_peaks="3",
min_dist_peaks="8.0"),
"Inference-OneTailed":
dict(comment="Inference: one-tailed",
inference_id="niiri:inference_id",
label="Inference",
alternative_hyp=NIDM_ONE_TAILED_TEST,
stat_map_id="niiri:statistic_map_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
inference_mask_id="niiri:mask_id_3",
display_mask_id="niiri:display_map_id",
mask_id="niiri:mask_id",
software_id="niiri:software_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id"),
"Inference-TwoTailed":
dict(comment="Inference: two-tailed",
inference_id="niiri:inference_id",
label="Inference",
alternative_hyp=NIDM_TWO_TAILED_TEST,
stat_map_id="niiri:statistic_map_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
inference_mask_id="niiri:mask_id_3",
display_mask_id="niiri:display_map_id",
mask_id="niiri:mask_id",
software_id="niiri:software_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id"),
"ConjunctionInference":
dict(comment="Conjunction Inference",
conj_inference_id="niiri:inference_id",
label="Conjunction Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id_1="niiri:statistic_map_id",
stat_map_id_2="niiri:statistic_map_id_2",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
display_mask_id="niiri:display_map_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"),
"SPM_KConjunctionInference":
dict(comment="SPM's Partial Conjunction Inference",
conj_inference_id="niiri:conjunction_id_2",
label="SPM's Partial Conjunction Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id_1="niiri:statistic_map_id_1",
stat_map_id_2="niiri:statistic_map_id_2",
global_null_degree="1",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
display_mask_id="niiri:display_map_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"),
"ExcursionSetMap":
dict(comment="Excursion Set Map",
id="niiri:excursion_set_map_id",
label="Excursion Set Map",
location="ExcursionSet.nii.gz",
format="image/nifti",
filename="ExcursionSet.nii.gz",
cluster_label_map_id="niiri:cluster_label_map_id",
max_intensity_projection_id="niiri:maximum_intensity_projection_\
id",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
num_of_clusters="8",
p_value="8.95949980872501e-14",
inference_id="niiri:inference_id"),
"SupraThresholdCluster":
dict(comment="Supra-Threshold Cluster",
cluster_id="niiri:supra_threshold_cluster_0001",
label="Supra-Threshold Cluster 0001",
cluster_size_in_voxels="530",
cluster_label_id="1",
cluster_size_in_resels="23.1209189500945",
p_value_unc="9.56276736481136e-52",
p_value_fwe="0",
p_value_fdr="7.65021389184909e-51",
excursion_set_id="niiri:excursion_set_map_id"),
"Peak_ValueP":
dict(comment="Peak",
peak_id="niiri:peak_0001",
label="Peak 0001",
location="niiri:coordinate_0001",
value="13.9346199035645",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="6.3705194444993e-11",
cluster_id="niiri:supra_threshold_cluster_0001"),
"Coordinate":
dict(comment="Coordinate",
coordinate_id="niiri:coordinate_0001",
label="Coordinate: 0001",
coord="[ -60, -28, 13 ]"),
"SearchSpaceMaskMap":
dict(comment="Search Space Mask Map",
search_space_id="niiri:search_space_mask_id",
location="SearchSpaceMask.nii.gz",
filename="SearchSpaceMask.nii.gz",
label="Search Space Mask Map",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_2",
expected_num_voxels="0.553331387916112",
expected_num_clusters="0.0889172687960151",
height_critical_fwe05="5.23529984739211",
height_critical_fdr05="6.22537899017334",
smallest_size_fwe05="1",
smallest_size_fdr05="3",
search_vol_voxels="65593",
search_vol_units="1771011",
resel_size="22.9229643140043",
search_vol_resels="2552.68032521656",
search_vol_resels_geom="[3, 72.3216126440484, 850.716735116472, \
2552.68032521656]",
noise_fwhm_in_voxels="[ 2.95881189165801, 2.96628446669584, \
2.61180425626264 ]",
noise_fwhm_in_units="[ 8.87643567497404, 8.89885340008753, \
7.83541276878791 ]",
random_field_station="false",
sha="e43b6e01b0463fe7d40782137867a",
inference_id="niiri:inference_id"),
"FSL_ClusterCenterOfGravity":
dict(
comment="Cluster Center Of Gravity",
center_of_gravity_id="niiri:center_of_gravity_1",
location="niiri:coordinate_0001",
label="Center of gravity",
cluster_id="niiri:supra_threshold_cluster_0001",
),
"CoordinateSpace":
dict(comment="Coordinate Space",
coordinate_space_id="niiri:coordinate_space_id_1",
label="Coordinate space 1",
voxel_to_world_mapping="[[-3, 0, 0, 78],[0, 3, 0, -112],\
[0, 0, 3, -50],[0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000051",
number_of_dim="3",
dimensions="[ 53, 63, 46 ]"),
"Image":
dict(comment="Image",
image_id="niiri:maximum_intensity_projection_id",
location="MaximumIntensityProjection.png",
filename="MaximumIntensityProjection.png",
format="image/png"),
"GrandMeanMap":
dict(comment="Grand Mean Map",
grand_mean_map_id="niiri:grand_mean_map_id",
label="Grand Mean Map",
location="GrandMean.nii.gz",
filename="GrandMean.nii.gz",
format="image/nifti",
masked_median="115",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
model_pe_id="niiri:model_pe_id"),
"SPM_DriftModel":
dict(comment="SPM's DCT Drift Model",
id="niiri:drift_model_id",
label="SPM's DCT Drift Model",
cut_off="128"),
"FSL_DriftModel":
dict(comment="FSL's Gaussian Running Line Drift Model",
id="niiri:drift_model_id",
label="FSL's Gaussian Running Line Drift Model",
cut_off="2"),
"ClusterDefinitionCriteria-06":
dict(comment="Cluster connectivity: face",
cluster_definition_criteria_id="niiri:cluster_definition_criteria\
_id",
label="Cluster Connectivity Criterion: 6",
connectivity="nidm:NIDM_0000130"),
"ClusterDefinitionCriteria-18":
dict(comment="Cluster connectivity: face or edge",
cluster_definition_criteria_id="niiri:cluster_definition_criteria\
_id",
label="Cluster Connectivity Criterion: 18",
connectivity="nidm:NIDM_0000128"),
"ClusterDefinitionCriteria-26":
dict(comment="Cluster connectivity: face, edge or corner",
cluster_definition_criteria_id="niiri:cluster_definition_criteria\
_id",
label="Cluster Connectivity Criterion: 26",
connectivity="nidm:NIDM_0000129")
}
# Delete old examples
shutil.rmtree(EX_DIR)
os.mkdir(EX_DIR)
example = ExampleFromTemplate(nidm_classes, EX_DIR, True)
example.create_example()
def main():
nidm_classes = {
"DesignMatrix":
dict(design_matrix_id='niiri:design_matrix_id',
label="Design Matrix",
location="file://path/to/DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id"),
"Image-DesignMatrix":
dict(image_id="niiri:design_matrix_png_id",
location="file://path/to/DesignMatrix.png",
filename="DesignMatrix.png",
format="image/png"),
"Data":
dict(data_id='niiri:data_id',
label="Data",
scaling="true",
target="10000"),
"ErrorModel":
dict(error_model_id="niiri:error_model_id",
noise_distribution="obo:STATO_0000227",
variance_homo="true",
variance_spatial="nidm:NIDM_0000073",
dependence="nidm:NIDM_0000048",
dependence_spatial="nidm:NIDM_0000073"),
"ModelParametersEstimation":
dict(model_pe_id="niiri:model_pe_id",
label="Model parameters estimation",
est_method=STATO_OLS_STR,
est_method_comment=STATO_OLS_LABEL,
design_matrix_id="niiri:design_matrix_id",
data_matrix_id="niiri:data_id",
error_model_id="niiri:error_model_id",
software_id="niiri:software_id"),
"ParameterEstimateMap_Location-1":
dict(beta_map_id="niiri:beta_map_id_1",
label="Parameter estimate 1",
location="file://path/to/ParameterEstimate_0001.nii.gz",
filename="ParameterEstimate_0001.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="f51b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_pe_id"),
"ParameterEstimateMap_Location-2":
dict(beta_map_id="niiri:beta_map_id_2",
label="Parameter estimate 2",
location="file://path/to/ParameterEstimate_0002.nii.gz",
filename="ParameterEstimate_0002.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="p89b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_pe_id"),
"CoordinateSpace-1":
dict(coordinate_space_id="niiri:coordinate_space_id_1",
label="Coordinate space 1",
voxel_to_world_mapping=
"[[-3, 0, 0, 81],[0, 3, 0, -115],[0, 0, 3, -53],[0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000047",
number_of_dim="3",
dimensions="[ 53, 63, 46 ]"),
"CoordinateSpace-2":
dict(coordinate_space_id="niiri:coordinate_space_id_2",
label="Coordinate space 2",
voxel_to_world_mapping=
"[[-3, 0, 0, 81],[0, 3, 0, -115],[0, 0, 3, -53],[0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000047",
number_of_dim="3",
dimensions="[ 53, 63, 46 ]"),
"ResidualMeanSquaresMap":
dict(residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
label="Residual Mean Squares Map",
location="file://path/to/ResidualMeanSquares.nii.gz",
filename="ResidualMeanSquares.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
param_est_id="niiri:model_pe_id"),
"MaskMap_Analysis":
dict( # The analysis mask
mask_id="niiri:mask_id_1",
label="Mask",
location="file://path/to/Mask.nii.gz",
filename="Mask.nii.gz",
user_defined="false",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
generated_by_act_id="niiri:model_pe_id",
used_by_act_id="niiri:contrast_estimation_id"),
"ContrastWeights":
dict(contrast_id="niiri:contrast_id",
label="Contrast weights: listening > rest",
value="[ 1, 0, 0 ]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > rest"),
"ContrastEstimation":
dict(contrast_estimation_id="niiri:contrast_estimation_id",
label="Contrast estimation",
software_id="niiri:software_id",
mask_id="niiri:mask_id_1",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id",
param_est_map="niiri:beta_map_id_1"),
"ContrastEstUsedParamEst-1-2":
dict(contrast_estimation_id="niiri:contrast_estimation_id",
param_est_map="niiri:beta_map_id_2"),
"ContrastMap":
dict(
contrast_map_id="niiri:contrast_map_id",
label="Contrast Map: listening > rest",
location="file://path/to/Contrast.nii.gz",
format="image/nifti",
filename="Contrast.nii.gz",
contrast_name="listening > rest",
coordinate_space_id="niiri:coordinate_space_id_1",
sha=
"400a2f07d99ed9be06577e6ecc89222cf4b688c654bc89067da558e88b73b97dd1b25e6c98f2a735fa0a1409598cff7e6025bda55abb6b9f5ef65d8d307eeba8",
contrast_est_id="niiri:contrast_estimation_id"),
"ContrastStandardErrorMap":
dict(contrast_standard_error_map_id=
"niiri:contrast_standard_error_map_id",
label="Contrast Standard Error Map",
location="file://path/to/ContrastStandardError.nii.gz",
format="image/nifti",
filename="ContrastStandardError.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
contrast_est_id="niiri:contrast_estimation_id"),
"FSL_DerivedMap-ContrastVariance":
dict(derived_from_map_id="niiri:contrast_variance_map_id",
derived_map_type="nidm:NIDM_0000135",
filename="varcope1.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
map_id="niiri:contrast_standard_error_map_id"),
"StatisticMap":
dict(
statistic_map_id="niiri:statistic_map_id",
label="Statistic Map: listening > rest",
location="file://path/to/TStatistic_0001.nii.gz",
format="image/nifti",
filename="TStatistic_0001.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > rest",
error_dof="73.0",
effect_dof="1",
sha=
"400a2f07d99ed9be06577e6ecc89222cf4b688c654bc89067da558e88b73b97dd1b25e6c98f2a735fa0a1409598cff7e6025bda55abb6b9f5ef65d8d307eeba8",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id"),
"StatisticMap-Z":
dict(
statistic_map_id="niiri:z_statistic_map_id",
label="Z-Statistic Map: listening > rest",
location="file://path/to/ZStatistic_0001.nii.gz",
format="image/nifti",
filename="ZStatistic_0001.nii.gz",
statistic_type=STATO_ZSTATISTIC_STR,
contrast_name="listening > rest",
error_dof="INF",
effect_dof="1",
sha=
"400a2f07d99ed9be06577e6ecc89222cf4b688c654bc89067da558e88b73b97dd1b25e6c98f2a735fa0a1409598cff7e6025bda55abb6b9f5ef65d8d307eeba8",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id"),
"HeightThreshold_equivThresh_equivThresh2":
dict(height_threshold_id="niiri:height_threshold_id",
thresh_type=OBO_P_VALUE_FWER_QNAME,
label="Height Threshold: p<0.05 (FWE)",
value="0.05",
equiv_thresh="niiri:height_threshold_id_2",
equiv_thresh2="niiri:height_threshold_id_3"),
"HeightThreshold-2":
dict(height_threshold_id="niiri:height_threshold_id_2",
thresh_type=OBO_STATISTIC_QNAME,
label="Height Threshold",
value="5.235300"),
"HeightThreshold-3":
dict(
height_threshold_id="niiri:height_threshold_id_3",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
label="Height Threshold",
value="0.000001",
),
"ExtentThreshold":
dict(
extent_threshold_id="niiri:extent_threshold_id",
label="Cluster Threshold",
thresh_type=OBO_P_VALUE_FWER_QNAME,
value="1",
),
"DisplayMaskMap":
dict(display_map_id="niiri:display_map_id",
label="Display Mask Map",
location="file://path/to/DisplayMask.nii.gz",
format="image/nifti",
user_defined="true",
filename="DisplayMask.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_2",
sha="e43b6e01b0463fe7d40782137867a"),
"PeakDefinitionCriteria_MaxPeaks":
dict(peak_definition_criteria_id="niiri:peak_definition_criteria_id",
label="Peak Definition Criteria",
max_num_peaks="3",
min_dist_peaks="8.0"),
"ClusterDefinitionCriteria":
dict(cluster_definition_criteria_id=
"niiri:cluster_definition_criteria_id",
label="Cluster Connectivity Criterion: 18",
connectivity="nidm:NIDM_0000128"),
"Inference":
dict(inference_id="niiri:inference_id",
label="Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id="niiri:z_statistic_map_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
display_mask_id="niiri:display_map_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"),
"FSL_ExcursionSetMap":
dict(
id="niiri:excursion_set_map_id",
label="Excursion Set Map",
location="file://path/to/ExcursionSet.nii.gz",
format="image/nifti",
filename="ExcursionSet.nii.gz",
cluster_label_map_id="niiri:cluster_label_map_id",
png_id="niiri:excursion_set_png_id_1",
coordinate_space_id="niiri:coordinate_space_id_1",
sha=
"400a2f07d99ed9be06577e6ecc89222cf4b688c654bc89067da558e88b73b97dd1b25e6c98f2a735fa0a1409598cff7e6025bda55abb6b9f5ef65d8d307eeba8",
inference_id="niiri:inference_id"),
"Image":
dict(image_id="niiri:excursion_set_png_id_1",
location="file://path/to/rendered_thresh_zstat1.png",
filename="rendered_thresh_zstat1.png",
format="image/png"),
"FSL_SupraThresholdCluster-1":
dict(cluster_id="niiri:supra_threshold_cluster_0001",
label="Supra-Threshold Cluster 0001",
cluster_size_in_voxels="530",
cluster_label_id="1",
p_value_fwe="0.000000",
excursion_set_id="niiri:excursion_set_map_id"),
"FSL_ClusterCenterOfGravity-1":
dict(center_of_gravity_id="niiri:center_of_gravity_1",
label="Center of gravity 1",
location="niiri:COG_coordinate_0001",
cluster_id="niiri:supra_threshold_cluster_0001"),
"FSL_Coordinate-COG1":
dict(
coordinate_id="niiri:COG_coordinate_0001",
label="Coordinate 1",
coord="[ 40.2, 16.4, 13.2 ]",
coord_in_vox="[ -30.8, -68.5, -13.4 ]",
),
"FSL_SupraThresholdCluster-2":
dict(cluster_id="niiri:supra_threshold_cluster_0002",
label="Supra-Threshold Cluster 0002",
cluster_size_in_voxels="445",
cluster_label_id="2",
p_value_fwe="0.000000",
excursion_set_id="niiri:excursion_set_map_id"),
"FSL_ClusterCenterOfGravity-2":
dict(center_of_gravity_id="niiri:center_of_gravity_2",
label="Center of gravity 2",
location="niiri:COG_coordinate_0002",
cluster_id="niiri:supra_threshold_cluster_0002"),
"FSL_Coordinate-COG2":
dict(coordinate_id="niiri:COG_coordinate_0002",
label="Coordinate 2",
coord="[ 25.6, 12.8, 14.6 ]",
coord_in_vox="[ 24.1, -77.1, -4.27 ]"),
"Peak-M1":
dict(peak_id="niiri:peak_0001",
label="Peak 1",
p_uncorr="4.126074e-10",
location="niiri:coordinate_0001",
equiv_z="6.14",
cluster_id="niiri:supra_threshold_cluster_0001"),
"FSL_Coordinate-1":
dict(
coordinate_id="niiri:coordinate_0001",
label="Coordinate 1",
coord="[ -48.1, -73.7, -9.24 ]",
coord_in_vox="[ 45, 15, 14 ]",
),
"Peak-2":
dict(peak_id="niiri:peak_0002",
label="Peak 2",
p_uncorr="7.705712e-10",
location="niiri:coordinate_0002",
equiv_z="6.04",
cluster_id="niiri:supra_threshold_cluster_0001"),
"FSL_Coordinate-2":
dict(
coordinate_id="niiri:coordinate_0002",
label="Coordinate 2",
coord="[ -38.1, -53.4, -18 ]",
coord_in_vox="[ 42, 21, 13 ]",
),
"Peak-3":
dict(peak_id="niiri:peak_0003",
label="Peak 3",
p_uncorr="4.462172e-09",
location="niiri:coordinate_0003",
equiv_z="5.75",
cluster_id="niiri:supra_threshold_cluster_0001"),
"FSL_Coordinate-3":
dict(
coordinate_id="niiri:coordinate_0003",
label="Coordinate 3",
coord="[ -29.6, -73.8, -16.9 ]",
coord_in_vox="[ 40, 15, 12 ]",
),
"Peak-4":
dict(peak_id="niiri:peak_0004",
label="Peak 4",
p_uncorr="4.462172e-09",
location="niiri:coordinate_0004",
equiv_z="5.75",
cluster_id="niiri:supra_threshold_cluster_0001"),
"FSL_Coordinate-4":
dict(coordinate_id="niiri:coordinate_0004",
label="Coordinate 4",
coord="[ 0.791, -87.2, 3.23 ]",
coord_in_vox="[ 39, 13, 12 ]"),
"Peak-M5":
dict(peak_id="niiri:peak_0005",
label="Peak 5",
p_uncorr="2.178976e-09",
location="niiri:coordinate_0005",
equiv_z="5.87",
cluster_id="niiri:supra_threshold_cluster_0002"),
"FSL_Coordinate-5":
dict(coordinate_id="niiri:coordinate_0005",
label="Coordinate 5",
coord="[ 16.1, -96.6, 5.82 ]",
coord_in_vox="[ 32, 10, 16 ]"),
"Peak-6":
dict(peak_id="niiri:peak_0006",
label="Peak 6",
p_uncorr="8.022392e-09",
location="niiri:coordinate_0006",
equiv_z="5.65",
cluster_id="niiri:supra_threshold_cluster_0002"),
"FSL_Coordinate-6":
dict(coordinate_id="niiri:coordinate_0006",
label="Coordinate 6",
coord="[ -25.5, -80.4, 15.3 ]",
coord_in_vox="[ 28, 7, 16 ]"),
"FSL_SearchSpaceMaskMap":
dict(
search_space_id="niiri:search_space_mask_id",
location="file://path/to/SearchSpaceMask.nii.gz",
filename="SearchSpaceMask.nii.gz",
label="Search Space Mask Map",
user_defined="false",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_2",
search_vol_voxels="45359",
search_vol_units="1.93808e+06",
search_vol_resels="3753.84",
resel_size="12.2251",
noise_roughness="0.384676",
random_field_station="true",
sha=
"400a2f07d99ed9be06577e6ecc89222cf4b688c654bc89067da558e88b73b97dd1b25e6c98f2a735fa0a1409598cff7e6025bda55abb6b9f5ef65d8d307eeba8",
inference_id="niiri:inference_id",
noise_fwhm_in_voxels="[2.38803, 2.43263, 2.07288]",
noise_fwhm_in_units="[8.35811, 8.5142, 7.2551]"),
"NIDMBundle":
dict(bundle_id="niiri:fsl_results_id",
label="NIDM-Results",
object_model="nidm:NIDM_0000027",
version="1.1.0",
time="2014-05-19T10:30:00.000+01:00",
export_id="niiri:export_id"),
"FSL_Software":
dict(software_id="niiri:software_id",
software_type="nlx:birnlex_2067",
label="FSL",
version="5.0.x",
feat_version="6.00"),
"ExporterSoftware":
dict(software_id="niiri:exporter_id",
software_type="nidm:NIDM_0000167",
label="nidmfsl",
version="0.2.0"),
"Export":
dict(export_id="niiri:export_id",
label="NIDM-Results export",
exporter_id="niiri:exporter_id"),
"GrandMeanMap":
dict(grand_mean_map_id="niiri:grand_mean_map_id",
label="Grand Mean Map",
location="file://path/to/GrandMean.nii.gz",
filename="GrandMean.nii.gz",
format="image/nifti",
masked_median="115",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a",
model_pe_id="niiri:model_pe_id")
}
NIDM_FSL_DIR = os.path.join(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'fsl')
ttl_file = os.path.join(NIDM_FSL_DIR, 'fsl_results.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def main():
nidm_classes = {
"DesignMatrix": dict(
design_matrix_id="niiri:design_matrix_id",
label="Design Matrix",
location="file:///path/to/DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id",
),
"Image-DesignMatrix": dict(
image_id="niiri:design_matrix_png_id",
location="file:///path/to/DesignMatrix.png",
filename="DesignMatrix.png",
format="image/png",
),
"Data": dict(data_id="niiri:data_id", label="Data", scaling="true", target=100),
"ErrorModel": dict(
error_model_id="niiri:error_model_id",
noise_distribution="nidm:NIDM_0000032",
variance_homo="true",
variance_spatial="nidm:NIDM_0000073",
dependence="nidm:NIDM_0000048",
dependence_spatial="nidm:NIDM_0000073",
),
"ModelParametersEstimation": dict(
model_pe_id="niiri:model_pe_id",
label="Model parameters estimation",
est_method=STATO_OLS_STR,
est_method_comment=STATO_OLS_LABEL,
design_matrix_id="niiri:design_matrix_id",
data_matrix_id="niiri:data_id",
error_model_id="niiri:error_model_id",
software_id="niiri:software_id",
),
"ParameterEstimateMap_Location-1": dict(
beta_map_id="niiri:beta_map_id_1",
label="Beta Map 1",
location="file:///path/to/ParameterEstimate_0001.nii.gz",
filename="ParameterEstimate_0001.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_pe_id",
),
"DerivedMap-PE1": dict(
derived_from_map_id="niiri:beta_map_id_1_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0001.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:beta_map_id_1",
),
"ParameterEstimateMap_Location-2": dict(
beta_map_id="niiri:beta_map_id_2",
label="Beta Map 2",
location="file:///path/to/ParameterEstimate_0002.nii.gz",
filename="ParameterEstimate_0002.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_pe_id",
),
"DerivedMap-PE2": dict(
derived_from_map_id="niiri:beta_map_id_2_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0002.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:beta_map_id_2",
),
"ParameterEstimateMap_Location-3": dict(
beta_map_id="niiri:beta_map_id_3",
label="Beta Map 3",
location="file:///path/to/ParameterEstimate_0003.nii.gz",
filename="ParameterEstimate_0003.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_pe_id",
),
"DerivedMap-PE3": dict(
derived_from_map_id="niiri:beta_map_id_3_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0003.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:beta_map_id_3",
),
"CoordinateSpace-1": dict(
coordinate_space_id="niiri:coordinate_space_id_1",
label="Coordinate space 1",
voxel_to_world_mapping="[[-3, 0, 0, 78],[0, 3, 0, -112],[0, 0, 3, -50],[0, 0, 0, 1]]",
voxel_units='[ \\"mm\\", \\"mm\\", \\"mm\\" ]',
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000051",
number_of_dim="3",
dimensions="[ 53, 63, 46 ]",
),
"ResidualMeanSquaresMap": dict(
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
label="Residual Mean Squares Map",
location="file:///path/to/ResidualMeanSquares.nii.gz",
filename="ResidualMeanSquares.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_pe_id",
),
"MaskMap_Analysis": dict( # The analysis mask
mask_id="niiri:mask_id_1",
label="Mask",
location="file:///path/to/Mask.nii.gz",
filename="Mask.nii.gz",
format="image/nifti",
user_defined="false",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
generated_by_act_id="niiri:model_pe_id",
used_by_act_id="niiri:contrast_estimation_id",
),
"ContrastWeights": dict(
contrast_id="niiri:contrast_id",
label="Contrast: listening > reading",
value="[1, -1, 0, 0]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > reading",
),
"ContrastWeights-2": dict(
contrast_id="niiri:contrast_id_2",
label="Contrast: motor",
value="[ 0, 0, 1 ]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="motor",
),
"ContrastEstimation": dict(
contrast_estimation_id="niiri:contrast_estimation_id",
label="Contrast estimation 1",
software_id="niiri:software_id",
mask_id="niiri:mask_id_1",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id",
param_est_map="niiri:beta_map_id_1",
),
"ContrastEstUsedParamEst-Con1PE2": dict(
contrast_estimation_id="niiri:contrast_estimation_id", param_est_map="niiri:beta_map_id_2"
),
"ContrastEstimation-2": dict(
contrast_estimation_id="niiri:contrast_estimation_id_2",
label="Contrast estimation 2",
software_id="niiri:software_id",
mask_id="niiri:mask_id_1",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id_2",
param_est_map="niiri:beta_map_id_3",
),
"ContrastEstUsedParamEst-Con2PE3": dict(
contrast_estimation_id="niiri:contrast_estimation_id_2", param_est_map="niiri:beta_map_id_3"
),
"ContrastMap": dict(
contrast_map_id="niiri:contrast_map_id",
label="Contrast Map: listening > reading",
location="file:///path/to/Contrast_0001.nii.gz",
format="image/nifti",
filename="Contrast_0001.nii.gz",
contrast_name="listening > reading",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
contrast_est_id="niiri:contrast_estimation_id",
),
"ContrastMap-2": dict(
contrast_map_id="niiri:contrast_map_id_2",
label="Contrast Map: motor",
location="file:///path/to/Contrast_0002.nii.gz",
format="image/nifti",
filename="Contrast_0002.nii.gz",
contrast_name="motor",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
contrast_est_id="niiri:contrast_estimation_id_2",
),
"DerivedMap-ContrastMap-2": dict(
derived_from_map_id="niiri:contrast_map_id_2_der",
derived_map_type="nidm:NIDM_0000002",
filename="con_0002.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:contrast_map_id_2",
),
"ContrastStandardErrorMap": dict(
contrast_standard_error_map_id="niiri:contrast_standard_error_map_id",
label="Contrast 1 Standard Error Map",
location="file:///path/to/ContrastStandardError_0001.nii.gz",
format="image/nifti",
filename="ContrastStandardError_0001.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
contrast_est_id="niiri:contrast_estimation_id",
),
"ContrastStandardErrorMap-2": dict(
contrast_standard_error_map_id="niiri:contrast_standard_error_map_id_2",
label="Contrast 2 Standard Error Map",
location="file:///path/to/ContrastStandardError_0002.nii.gz",
format="image/nifti",
filename="ContrastStandardError_0002.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
contrast_est_id="niiri:contrast_estimation_id_2",
),
"StatisticMap_T": dict(
statistic_map_id="niiri:statistic_map_id",
label="Statistic Map: listening > reading",
location="file:///path/to/TStatistic_0001.nii.gz",
format="image/nifti",
filename="TStatistic_0001.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > reading",
error_dof="72.9999999990787",
effect_dof="1",
sha="e43b6e01b0463fe7d40782137867a...",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id",
),
"DerivedMap-StatMap": dict(
derived_from_map_id="niiri:statistic_map_id_der",
derived_map_type="nidm:NIDM_0000076",
filename="spmT_0001.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:statistic_map_id",
),
"StatisticMap_T-2": dict(
statistic_map_id="niiri:statistic_map_id_2",
label="Statistic Map: motor",
location="file:///path/to/TStatistic_0002.nii.gz",
format="image/nifti",
filename="TStatistic_0002.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="motor",
error_dof="72.9999999990787",
effect_dof="1",
sha="e43b6e01b0463fe7d40782137867a...",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id_2",
),
"DerivedMap-StatMap-2": dict(
derived_from_map_id="niiri:statistic_map_id_2_der",
derived_map_type="nidm:NIDM_0000076",
filename="spmT_0002.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:statistic_map_id_2",
),
"HeightThreshold_equivThresh_equivThresh2": dict(
height_threshold_id="niiri:height_threshold_id",
thresh_type=OBO_P_VALUE_FWER_QNAME,
label="Height Threshold: p<0.05 (FWE)",
value="0.05",
equiv_thresh="niiri:height_threshold_id_12",
equiv_thresh2="niiri:height_threshold_id_13",
),
"HeightThreshold-12": dict(
height_threshold_id="niiri:height_threshold_id_12",
thresh_type=OBO_STATISTIC_QNAME,
label="Height Threshold",
value="5.23529984739211",
),
"HeightThreshold-13": dict(
height_threshold_id="niiri:height_threshold_id_13",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
label="Height Threshold",
value="7.62276079258051e-07",
),
"HeightThreshold_equivThresh_equivThresh2-2": dict(
height_threshold_id="niiri:height_threshold_id_2",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
label="Height Threshold: p<0.001 (unc)",
value="7.62276079258051e-07",
equiv_thresh="niiri:height_threshold_id_22",
equiv_thresh2="niiri:height_threshold_id_23",
),
"HeightThreshold-22": dict(
height_threshold_id="niiri:height_threshold_id_22",
thresh_type=OBO_STATISTIC_QNAME,
label="Height Threshold",
value="5.23529984739211",
),
"HeightThreshold-23": dict(
height_threshold_id="niiri:height_threshold_id_23",
thresh_type=OBO_P_VALUE_FWER_QNAME,
label="Height Threshold",
value="0.05",
),
"HeightThreshold_equivThresh_equivThresh2-3": dict(
height_threshold_id="niiri:height_threshold_id_3",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
label="Height Threshold: p<0.001 (unc)",
value="7.62276079258051e-07",
equiv_thresh="niiri:height_threshold_id_32",
equiv_thresh2="niiri:height_threshold_id_33",
),
"HeightThreshold-32": dict(
height_threshold_id="niiri:height_threshold_id_32",
thresh_type=OBO_STATISTIC_QNAME,
label="Height Threshold",
value="5.23529984739211",
),
"HeightThreshold-33": dict(
height_threshold_id="niiri:height_threshold_id_33",
thresh_type=OBO_P_VALUE_FWER_QNAME,
label="Height Threshold",
value="0.05",
),
"ExtentThresholdStat_equivThresh_equivThresh2_clusterSizeResels": dict(
extent_threshold_id="niiri:extent_threshold_id",
label="Extent Threshold: k>=0",
cluster_size_vox="0",
cluster_size_resels="0",
equiv_thresh="niiri:height_threshold_id_12",
equiv_thresh2="niiri:height_threshold_id_13",
),
"ExtentThreshold-12": dict(
extent_threshold_id="niiri:extent_threshold_id_12",
label="Extent Threshold",
thresh_type=OBO_P_VALUE_FWER_QNAME,
value="1",
),
"ExtentThreshold-13": dict(
extent_threshold_id="niiri:extent_threshold_id_13",
label="Extent Threshold",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
value="1",
),
"ExtentThresholdStat_equivThresh_equivThresh2_clusterSizeResels-2": dict(
extent_threshold_id="niiri:extent_threshold_id_2",
label="Extent Threshold: k>=5",
cluster_size_vox="5",
cluster_size_resels="1.6",
equiv_thresh="niiri:height_threshold_id_12",
equiv_thresh2="niiri:height_threshold_id_13",
),
"ExtentThreshold-22": dict(
extent_threshold_id="niiri:extent_threshold_id_22",
label="Extent Threshold",
thresh_type=OBO_P_VALUE_FWER_QNAME,
value="1",
),
"ExtentThreshold-23": dict(
extent_threshold_id="niiri:extent_threshold_id_23",
label="Extent Threshold",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
value="1",
),
"ExtentThresholdStat_equivThresh_equivThresh2_clusterSizeResels-3": dict(
extent_threshold_id="niiri:extent_threshold_id_3",
label="Extent Threshold: k>=10",
cluster_size_vox="10",
cluster_size_resels="3.3",
equiv_thresh="niiri:height_threshold_id_12",
equiv_thresh2="niiri:height_threshold_id_13",
),
"ExtentThreshold-32": dict(
extent_threshold_id="niiri:extent_threshold_id_32",
label="Extent Threshold",
thresh_type=OBO_P_VALUE_FWER_QNAME,
value="1",
),
"ExtentThreshold-33": dict(
extent_threshold_id="niiri:extent_threshold_id_33",
label="Extent Threshold",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
value="1",
),
"DisplayMaskMap": dict(
display_map_id="niiri:display_map_id",
label="Display Mask Map",
user_defined="true",
location="file:///path/to/DisplayMask.nii.gz",
filename="DisplayMask.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
),
"DisplayMaskMap-2": dict(
display_map_id="niiri:display_map_id_2",
label="Display Mask Map",
user_defined="true",
location="file:///path/to/DisplayMask.nii.gz",
format="image/nifti",
filename="DisplayMask.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
),
"DisplayMaskMap-3": dict(
display_map_id="niiri:display_map_id_3",
label="Display Mask Map",
user_defined="true",
location="file:///path/to/DisplayMask.nii.gz",
filename="DisplayMask.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
),
"PeakDefinitionCriteria_MaxPeaks": dict(
peak_definition_criteria_id="niiri:peak_definition_criteria_id",
label="Peak Definition Criteria",
max_num_peaks="3",
min_dist_peaks="8.0",
),
"PeakDefinitionCriteria_MaxPeaks-2": dict(
peak_definition_criteria_id="niiri:peak_definition_criteria_id_2",
label="Peak Definition Criteria",
max_num_peaks="3",
min_dist_peaks="8.0",
),
"PeakDefinitionCriteria_MaxPeaks-3": dict(
peak_definition_criteria_id="niiri:peak_definition_criteria_id_3",
label="Peak Definition Criteria",
max_num_peaks="3",
min_dist_peaks="8.0",
),
"ClusterDefinitionCriteria": dict(
cluster_definition_criteria_id="niiri:cluster_definition_criteria_id",
label="Cluster Connectivity Criterion: 18",
connectivity="nidm:NIDM_0000128",
),
"ClusterDefinitionCriteria-2": dict(
cluster_definition_criteria_id="niiri:cluster_definition_criteria_id_2",
label="Cluster Connectivity Criterion: 18",
connectivity="nidm:NIDM_0000128",
),
"ClusterDefinitionCriteria-3": dict(
cluster_definition_criteria_id="niiri:cluster_definition_criteria_id_3",
label="Cluster Connectivity Criterion: 18",
connectivity="nidm:NIDM_0000128",
),
"Inference": dict(
inference_id="niiri:inference_id",
label="Inference 1",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id="niiri:statistic_map_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
display_mask_id="niiri:display_map_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id",
),
"Inference-2": dict(
inference_id="niiri:inference_id_2",
label="Inference 2",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id="niiri:statistic_map_id_2",
height_thresh_id="niiri:height_threshold_id_2",
extent_thresh_id="niiri:extent_threshold_id_2",
display_mask_id="niiri:display_map_id_2",
peak_def_id="niiri:peak_definition_criteria_id_2",
cluster_def_id="niiri:cluster_definition_criteria_id_2",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id",
),
"ConjunctionInference": dict(
conj_inference_id="niiri:inference_id_3",
label="Conjunction Inference 3",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id_1="niiri:statistic_map_id",
stat_map_id_2="niiri:statistic_map_id_2",
height_thresh_id="niiri:height_threshold_id_3",
extent_thresh_id="niiri:extent_threshold_id_3",
display_mask_id="niiri:display_map_id_3",
peak_def_id="niiri:peak_definition_criteria_id_3",
cluster_def_id="niiri:cluster_definition_criteria_id_3",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id",
),
"DerivedMap-Contrast": dict(
derived_from_map_id="niiri:contrast_map_id_der",
derived_map_type="nidm:NIDM_0000002",
filename="con_0001.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:contrast_map_id",
),
"NIDMBundle": dict(
bundle_id="niiri:spm_results_id",
label="NIDM-Results",
object_model="nidm:NIDM_0000027",
version="1.1.0",
time="2014-05-19T10:30:00.000+01:00",
),
"SPM_ReselsPerVoxelMap": dict(
resels_per_voxel_map_id="niiri:resels_per_voxel_map_id",
label="Resels per Voxel Map",
location="file:///path/to/ReselsPerVoxel.nii.gz",
filename="ReselsPerVoxel.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
model_pe_id="niiri:model_pe_id",
),
"SPM_InferenceUsedRPVMap": dict(
inference_id="niiri:inference_id", resels_per_voxel_map_id="niiri:resels_per_voxel_map_id"
),
"SPM_InferenceUsedRPVMap-2": dict(
inference_id="niiri:inference_id_2", resels_per_voxel_map_id="niiri:resels_per_voxel_map_id"
),
"SPM_InferenceUsedRPVMap-3": dict(
inference_id="niiri:inference_id_3", resels_per_voxel_map_id="niiri:resels_per_voxel_map_id"
),
"DerivedMap-RPV": dict(
derived_from_map_id="niiri:resels_per_voxel_map_id_der",
derived_map_type="nidm:NIDM_0000144",
filename="RPV.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:resels_per_voxel_map_id",
),
"SPM_Software": dict(
software_id="niiri:software_id", software_type="nlx:nif-0000-00343", label="SPM", version="12b.5853"
),
"GrandMeanMap": dict(
grand_mean_map_id="niiri:grand_mean_map_id",
label="Grand Mean Map",
location="file:///path/to/GrandMean.nii.gz",
filename="GrandMean.nii.gz",
format="image/nifti",
masked_median="115",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
model_pe_id="niiri:model_pe_id",
),
}
NIDM_SPM_DIR = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "spm", "example002")
ttl_file = os.path.join(NIDM_SPM_DIR, "spm_results_2contrasts.ttl")
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def main():
nidm_classes = {
"ImagingInstrument": dict(
id="niiri:mr_scanner_id",
label="MRI Scanner",
type=q_graph.qname(NLX_MRI_SCANNER),
),
"DesignMatrix_1stLevel": dict(
design_matrix_id='niiri:design_matrix_id',
label="Design Matrix",
location="DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id",
regressors='[\\\"Sn(1) active*bf(1)\\\", \\\"Sn(1) constant\\\"]',
hrf_basis="spm:SPM_0000004",
drift_model="niiri:drift_model_id"),
"SPM_DriftModel": dict(
id="niiri:drift_model_id",
label="SPM's DCT Drift Model",
cut_off="128"
),
"Image-DesignMatrix": dict(
image_id="niiri:design_matrix_png_id",
location="DesignMatrix.png",
filename="DesignMatrix.png",
format="image/png"
),
"Person": dict(
id='niiri:subject_id',
label="Person"
),
"Data": dict(
data_id='niiri:data_id',
label="Data",
scaling="true",
target=100,
scanner_id="niiri:mr_scanner_id",
sub_or_group_id="niiri:subject_id",
mr_protocol=q_graph.qname(NLX_FMRI_PROTOCOL)
),
"ErrorModel": dict(
error_model_id="niiri:error_model_id",
noise_distribution="obo:STATO_0000227",
variance_homo="true",
variance_spatial="nidm:NIDM_0000073",
dependence="obo:STATO_0000357",
dependence_spatial="nidm:NIDM_0000072"
),
"ModelParametersEstimation": dict(
model_pe_id="niiri:model_pe_id",
label="Model parameters estimation",
est_method=STATO_GLS_STR,
est_method_comment=STATO_GLS_LABEL,
design_matrix_id="niiri:design_matrix_id",
data_matrix_id="niiri:data_id",
error_model_id="niiri:error_model_id",
software_id="niiri:software_id"
),
"ParameterEstimateMap-1": dict(
beta_map_id="niiri:beta_map_id_1",
label="Beta Map 1",
coordinate_space_id="niiri:coordinate_space_id_1",
param_est_id="niiri:model_pe_id"),
"DerivedMap-PE1": dict(
derived_from_map_id="niiri:beta_map_id_1_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0001.nii",
format="image/nifti",
sha="fab2573099693215bac756bc796fbc983524473dec5c1b2d66fb83694c174\
12731df7f574094cb6c4a77994af7be11ed9aa545090fbe8ec6565a5c3c3dae8f0f",
map_id="niiri:beta_map_id_1"
),
"ParameterEstimateMap-2": dict(
beta_map_id="niiri:beta_map_id_2",
label="Beta Map 2",
coordinate_space_id="niiri:coordinate_space_id_1",
param_est_id="niiri:model_pe_id"),
"CoordinateSpace-1": dict(
coordinate_space_id="niiri:coordinate_space_id_1",
label="Coordinate space 1",
voxel_to_world_mapping="[[-3, 0, 0, 78],[0, 3, 0, -112],[0, 0, 3, \
-70],[0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000051",
number_of_dim="3",
dimensions="[ 53, 63, 52 ]"),
"ResidualMeanSquaresMap": dict(
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
label="Residual Mean Squares Map",
location="ResidualMeanSquares.nii.gz",
filename="ResidualMeanSquares.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="84cd0e608b8763307a1166b88761291e552838d85b58334a69a286060f648\
9a3b0929a940c3ccac883803455118787ea32e0bb5a6d236a5d6e9e8b6a9f918a6b",
param_est_id="niiri:model_pe_id"),
"DerivedMap-RMSMap": dict(
derived_from_map_id="niiri:residual_mean_squares_map_id_der",
derived_map_type="nidm:NIDM_0000066",
filename="ResMS.nii",
format="image/nifti",
sha="1635e0ae420cac1b5989fbc753b95f504dd957ff2986367fc4cd13ff35c44\
b4ee60994a9cdcab93a7d247fc5a8decb7578fa4c553b0ac905af8c7041db9b4acd",
map_id="niiri:residual_mean_squares_map_id"
),
"MaskMap_Analysis": dict( # The "analysis mask"
mask_id="niiri:mask_id_1",
label="Mask",
location="Mask.nii.gz",
user_defined="false",
filename="Mask.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="932fd9f0d55e9822748f4a9b35a0a7f0fe442f3e061e2eda48c2617a2938d\
f50ea84deca8de0725641a0105b712a80a0c8931df9bdf3bef788b1041379d00875",
generated_by_act_id="niiri:model_pe_id",
used_by_act_id="niiri:contrast_estimation_id"),
"DerivedMap-Mask2": dict( # The "analysis mask" (derived)
derived_from_map_id="niiri:mask_id_1_der",
derived_map_type="nidm:NIDM_0000054",
filename="mask.nii",
format="image/nifti",
sha="fbc254cab29db5532feccce554ec9d3c845197eca9013ec9f0efd5d8d56e3\
aa008ccee4038fb3651d30447fa0f316938b07c3ad961b623458dcd9b46968a8e11",
map_id="niiri:mask_id_1"
),
"ContrastWeights": dict(
contrast_id="niiri:contrast_id",
label="Contrast: passive listening > rest",
value="[1, 0]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="passive listening > rest"
),
"ContrastEstimation": dict(
contrast_estimation_id="niiri:contrast_estimation_id",
label="Contrast estimation",
software_id="niiri:software_id",
mask_id="niiri:mask_id_1",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id",
param_est_map="niiri:beta_map_id_1"
),
"ContrastEstUsedParamEst-Con1PE2": dict(
contrast_estimation_id="niiri:contrast_estimation_id",
param_est_map="niiri:beta_map_id_2"
),
"ContrastMap": dict(
contrast_map_id="niiri:contrast_map_id",
label="Contrast Map: passive listening > rest",
location="Contrast.nii.gz",
format="image/nifti",
filename="Contrast.nii.gz",
contrast_name="passive listening > rest",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="f0720b732aaf19c2ec42d0469f8308beb3aa978baf65c7dce6476a0d8e5b2\
f38c4fa9609f045a536678440feebce9a047e3bd6d59fdb8fb64baae058690bbda2",
contrast_est_id="niiri:contrast_estimation_id"),
"ContrastStandardErrorMap": dict(
contrast_standard_error_map_id="niiri:contrast_standard_error_map_\
id",
label="Contrast Standard Error Map",
location="ContrastStandardError.nii.gz",
format="image/nifti",
filename="ContrastStandardError.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="f4e3616579fe8b0812469409b1501e391bb17ca6e364f37d622b37fa9014c\
f1dd89befece07e73cf5bca5b3116f55ac4496751ca990db85e8377001a4be941b2",
contrast_est_id="niiri:contrast_estimation_id"),
"StatisticMap_T": dict(
statistic_map_id="niiri:statistic_map_id",
label="Statistic Map: passive listening > rest",
location="TStatistic.nii.gz",
format="image/nifti",
filename="TStatistic.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="passive listening > rest",
error_dof="84.0",
effect_dof="1",
sha="799e9bbf8c15b35c0098bca468846bf2cd895a3366382b5ceaa953f1e9e57\
6955341a7c86e13e6fe9359da4ff1496a609f55ce9ecff8da2e461365372f2506d6",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id"),
"DerivedMap-StatMap": dict(
derived_from_map_id="niiri:statistic_map_id_der",
derived_map_type="nidm:NIDM_0000076",
filename="spmT_0001.nii",
format="image/nifti",
sha="55951f31f0ede7e88eca5cd4793df3f630aba21bc90fb81e3695db060c7d\
4c0b0ccf0b51fd8958c32ea3253d3122e9b31a54262bf910f8b5b646054ceb9a5825",
map_id="niiri:statistic_map_id"
),
"HeightThreshold_equivThresh_equivThresh2": dict(
height_threshold_id="niiri:height_threshold_id",
thresh_type=OBO_P_VALUE_FWER_QNAME,
label="Height Threshold: p<0.05 (FWE)",
value="0.0499999999999976",
equiv_thresh="niiri:height_threshold_id_2",
equiv_thresh2="niiri:height_threshold_id_3"
),
"HeightThreshold-2": dict(
height_threshold_id="niiri:height_threshold_id_2",
thresh_type=OBO_STATISTIC_QNAME,
label="Height Threshold",
value="4.85241745689539"
),
"HeightThreshold-3": dict(
height_threshold_id="niiri:height_threshold_id_3",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
label="Height Threshold",
value="2.7772578456986e-06",
),
"ExtentThresholdStat_equivThresh_equivThresh2_clusterSizeResels": dict(
extent_threshold_id="niiri:extent_threshold_id",
label="Extent Threshold: k>=0",
cluster_size_vox="0",
cluster_size_resels="0",
equiv_thresh="niiri:extent_threshold_id_2",
equiv_thresh2="niiri:extent_threshold_id_3"
),
"ExtentThreshold-2": dict(
extent_threshold_id="niiri:extent_threshold_id_2",
label="Extent Threshold",
thresh_type=OBO_P_VALUE_FWER_QNAME,
value="1",
),
"ExtentThreshold-3": dict(
extent_threshold_id="niiri:extent_threshold_id_3",
label="Extent Threshold",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
value="1",
),
"PeakDefinitionCriteria_MaxPeaks": dict(
peak_definition_criteria_id="niiri:peak_definition_criteria_id",
label="Peak Definition Criteria",
max_num_peaks="3",
min_dist_peaks="8.0"
),
"ClusterDefinitionCriteria": dict(
cluster_definition_criteria_id="niiri:cluster_definition_criteria\
_id",
label="Cluster Connectivity Criterion: 18",
connectivity="nidm:NIDM_0000128"
),
"Inference": dict(
inference_id="niiri:inference_id",
label="Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id="niiri:statistic_map_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
Inference_mask_id="niiri:sub_volume_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"
),
"ExcursionSetMap": dict(
id="niiri:excursion_set_map_id",
label="Excursion Set Map",
location="ExcursionSet.nii.gz",
format="image/nifti",
filename="ExcursionSet.nii.gz",
cluster_label_map_id="niiri:cluster_label_map_id",
max_intensity_projection_id="niiri:maximum_intensity_projection\
_id",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="d96b82761c299a66978893cab6034f3f8aed25d0a135636b0ffe79f4cf11b\
ecce86ba261f7aeb43717f5d0e47ad0b14cfb0402786251e3f2c507890c83b27652",
num_of_clusters="5",
p_value="2.83510681598e-09",
inference_id="niiri:inference_id"
),
"SupraThresholdCluster-1": dict(
cluster_id="niiri:supra_threshold_cluster_0001",
label="Supra-Threshold Cluster: 0001",
cluster_size_in_voxels="839",
cluster_label_id="1",
cluster_size_in_resels="6.31265696809113",
p_value_unc="3.55896824480477e-19",
p_value_fwe="0",
p_value_fdr="1.77948412240239e-18",
excursion_set_id="niiri:excursion_set_map_id"
),
"SupraThresholdCluster-2": dict(
cluster_id="niiri:supra_threshold_cluster_0002",
label="Supra-Threshold Cluster: 0002",
cluster_size_in_voxels="695",
cluster_label_id="2",
cluster_size_in_resels="5.22919736927692",
p_value_unc="5.34280282632073e-17",
p_value_fwe="0",
p_value_fdr="1.33570070658018e-16",
excursion_set_id="niiri:excursion_set_map_id"
),
"SupraThresholdCluster-3": dict(
cluster_id="niiri:supra_threshold_cluster_0003",
label="Supra-Threshold Cluster: 0003",
cluster_size_in_voxels="37",
cluster_label_id="3",
cluster_size_in_resels="0.278388924695318",
p_value_unc="0.00497953247554004",
p_value_fwe="0.000255384009130943",
p_value_fdr="0.00829922079256674",
excursion_set_id="niiri:excursion_set_map_id"
),
"SupraThresholdCluster-4": dict(
cluster_id="niiri:supra_threshold_cluster_0004",
label="Supra-Threshold Cluster: 0004",
cluster_size_in_voxels="29",
cluster_label_id="4",
cluster_size_in_resels="0.218196724761195",
p_value_unc="0.0110257032104773",
p_value_fwe="0.000565384750377596",
p_value_fdr="0.0137821290130967",
excursion_set_id="niiri:excursion_set_map_id"
),
"SupraThresholdCluster-5": dict(
cluster_id="niiri:supra_threshold_cluster_0005",
label="Supra-Threshold Cluster: 0005",
cluster_size_in_voxels="12",
cluster_label_id="5",
cluster_size_in_resels="0.0902882999011843",
p_value_unc="0.0818393184514307",
p_value_fwe="0.00418900977248904",
p_value_fdr="0.0818393184514307",
excursion_set_id="niiri:excursion_set_map_id"
),
"Peak_ValueP-1": dict(
peak_id="niiri:peak_0001",
label="Peak: 0001",
location="niiri:coordinate_0001",
value="17.5207633972168",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="1.19156591713838e-11",
cluster_id="niiri:supra_threshold_cluster_0001"
),
"Coordinate-1": dict(
coordinate_id="niiri:coordinate_0001",
label="Coordinate: 0001",
coord="[ -60, -25, 11 ]"
),
"Peak_ValueP-2": dict(
peak_id="niiri:peak_0002",
label="Peak: 0002",
location="niiri:coordinate_0002",
value="13.0321407318",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="1.19156591714e-11",
cluster_id="niiri:supra_threshold_cluster_0001"
),
"Coordinate-2": dict(
coordinate_id="niiri:coordinate_0002",
label="Coordinate: 0002",
coord="[ -42, -31, 11 ]"
),
"Peak_ValueP-3": dict(
peak_id="niiri:peak_0003",
label="Peak: 0003",
location="niiri:coordinate_0003",
value="10.2856016159058",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="7.69451169446711e-12",
p_value_fdr="6.84121260274992e-10",
cluster_id="niiri:supra_threshold_cluster_0001"
),
"Coordinate-3": dict(
coordinate_id="niiri:coordinate_0003",
label="Coordinate: 0003",
coord="[ -66, -31, -1 ]"
),
"Peak_ValueP-4": dict(
peak_id="niiri:peak_0004",
label="Peak: 0004",
location="niiri:coordinate_0004",
value="13.5425577163696",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="1.19156591713838e-11",
cluster_id="niiri:supra_threshold_cluster_0002"
),
"Coordinate-4": dict(
coordinate_id="niiri:coordinate_0004",
label="Coordinate: 0004",
coord="[ 63, -13, -4 ]"
),
"Peak_ValueP-5": dict(
peak_id="niiri:peak_0005",
label="Peak: 0005",
location="niiri:coordinate_0005",
value="12.4728717803955",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="1.19156591713838e-11",
cluster_id="niiri:supra_threshold_cluster_0002"
),
"Coordinate-5": dict(
coordinate_id="niiri:coordinate_0005",
label="Coordinate: 0005",
coord="[ 60, -22, 11 ]"
),
"Peak_ValueP-6": dict(
peak_id="niiri:peak_0006",
label="Peak: 0006",
location="niiri:coordinate_0006",
value="9.72103404998779",
equiv_z="INF",
p_uncorr="1.22124532708767e-15",
p_value_fwe="6.9250605250204e-11",
p_value_fdr="6.52169693024352e-09",
cluster_id="niiri:supra_threshold_cluster_0002"
),
"Coordinate-6": dict(
coordinate_id="niiri:coordinate_0006",
label="Coordinate: 0006",
coord="[ 57, -40, 5 ]"
),
"Peak_ValueP-7": dict(
peak_id="niiri:peak_0007",
label="Peak: 0007",
location="niiri:coordinate_0007",
value="6.55745935440063",
equiv_z="5.87574033699266",
p_uncorr="2.10478867668229e-09",
p_value_fwe="9.17574302586877e-05",
p_value_fdr="0.00257605396646668",
cluster_id="niiri:supra_threshold_cluster_0003"
),
"Coordinate-7": dict(
coordinate_id="niiri:coordinate_0007",
label="Coordinate: 0007",
coord="[ 36, -28, -13 ]"
),
"Peak_ValueP-8": dict(
peak_id="niiri:peak_0008",
label="Peak: 0008",
location="niiri:coordinate_0008",
value="6.19558477401733",
equiv_z="5.60645028016544",
p_uncorr="1.0325913235576e-08",
p_value_fwe="0.000382453907303626",
p_value_fdr="0.00949154522981781",
cluster_id="niiri:supra_threshold_cluster_0004"
),
"Coordinate-8": dict(
coordinate_id="niiri:coordinate_0008",
label="Coordinate: 0008",
coord="[ -33, -31, -16 ]"
),
"Peak_ValueP-9": dict(
peak_id="niiri:peak_0009",
label="Peak: 0009",
location="niiri:coordinate_0009",
value="5.27320194244385",
equiv_z="4.88682085490477",
p_uncorr="5.12386299833523e-07",
p_value_fwe="0.0119099090973821",
p_value_fdr="0.251554254717758",
cluster_id="niiri:supra_threshold_cluster_0005"
),
"Coordinate-9": dict(
coordinate_id="niiri:coordinate_0009",
label="Coordinate: 0009",
coord="[ 45, -40, 32 ]"
),
"SearchSpaceMaskMap": dict( # The "search space"
search_space_id="niiri:search_space_mask_id",
location="SearchSpaceMask.nii.gz",
filename="SearchSpaceMask.nii.gz",
label="Search Space Mask Map",
format="image/nifti",
user_defined="false",
coordinate_space_id="niiri:coordinate_space_id_1",
expected_num_voxels="4.02834655908613",
expected_num_clusters="0.0512932943875478",
height_critical_fwe05="4.85241745689539",
height_critical_fdr05="5.7639536857605",
smallest_size_fwe05="12",
smallest_size_fdr05="29",
search_vol_voxels="69306",
search_vol_units="1871262",
resel_size="132.907586178202",
search_vol_resels="467.07642343881",
search_vol_resels_geom="[7, 42.96312274763, 269.40914815306, \
467.07642343881]",
noise_fwhm_in_voxels="[ 5.41278985910694, 5.43638957240286, \
4.51666658877481 ]",
noise_fwhm_in_units="[ 16.2383695773208, 16.3091687172086, \
13.5499997663244 ]",
random_field_station="true",
sha="932fd9f0d55e9822748f4a9b35a0a7f0fe442f3e061e2eda48c2617a2938\
df50ea84deca8de0725641a0105b712a80a0c8931df9bdf3bef788b1041379d00875",
inference_id="niiri:inference_id"
),
"DerivedMap": dict(
derived_from_map_id="niiri:contrast_map_id_der",
derived_map_type="nidm:NIDM_0000002",
filename="con_0001.nii",
format="image/nifti",
sha="277dd1da13d391c33c172fb8c71060008cc66e173de6362eb857b0055b41e\
9bae57911f7ec4b45659905103b1139ebf3da0c2d04cf105bbce0cdc3004b643c22",
map_id="niiri:contrast_map_id"
),
"DerivedMap-2": dict(
derived_from_map_id="niiri:beta_map_id_2_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0002.nii",
format="image/nifti",
sha="3f72b788762d9ab2c7ddb5e4d446872694ee42fc8897fe5317b54efb7924f\
784da6499065db897a49595d8763d1893ad65ad102b0c88f2e72e2d028173343008",
map_id="niiri:beta_map_id_2"
),
"NIDMBundle": dict(
bundle_id="niiri:spm_results_id",
label="NIDM-Results",
object_model="nidm:NIDM_0000027",
version="1.1.0",
time="2014-05-19T10:30:00.000+01:00",
export_id="niiri:export_id"
),
"SPM_ReselsPerVoxelMap": dict(
resels_per_voxel_map_id="niiri:resels_per_voxel_map_id",
label="Resels per Voxel Map",
location="ReselsPerVoxel.nii.gz",
filename="ReselsPerVoxel.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="2025dc6c33708b80708c2eba3215fb1149df236fb558a8e8f8f6cf34595fb\
54734fe5e436db3e192a424d99699dd7feb2f4a9020ceae8e7bcbd881b17825256a",
model_pe_id="niiri:model_pe_id"
),
"SPM_InferenceUsedRPVMap": dict(
inference_id="niiri:inference_id",
resels_per_voxel_map_id="niiri:resels_per_voxel_map_id"
),
"DerivedMap-RPVMap": dict(
derived_from_map_id="niiri:resels_per_voxel_map_id_der",
derived_map_type="nidm:NIDM_0000144",
filename="RPV.nii",
format="image/nifti",
sha="963283cdde607c40e4640c27453867bd0d70133b6d61482933862487c0f4a\
5acdb2e338a12a2605ee044b1aa47b5717f0c520b90ed3c49b5227f0483bd48512d",
map_id="niiri:resels_per_voxel_map_id"
),
"ClusterLabelsMap": dict(
cluster_label_map_id="niiri:cluster_label_map_id",
location="ClusterLabels.nii.gz",
filename="ClusterLabels.nii.gz",
format="image/nifti"
),
"SPM_Software": dict(
software_id="niiri:software_id",
software_type="scr:SCR_007037",
label="SPM",
version="12.12.1"
),
"Image": dict(
image_id="niiri:maximum_intensity_projection_id",
location="MaximumIntensityProjection.png",
filename="MaximumIntensityProjection.png",
format="image/png"
),
"GrandMeanMap": dict(
grand_mean_map_id="niiri:grand_mean_map_id",
label="Grand Mean Map",
location="GrandMean.nii.gz",
filename="GrandMean.nii.gz",
format="image/nifti",
masked_median="132.008995056152",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="4d3528031bce4a9c1b994b8124e6e0eddb9df90b49c84787652ed94df8c14\
c04ec92100a2d8ea86a8df24ba44617aca7457ddcb2f42253fc17e33296a1aea1cb",
model_pe_id="niiri:model_pe_id"
),
"ExporterSoftware": dict(
software_id="niiri:exporter_id",
software_type="nidm:NIDM_0000168",
label="spm_results_nidm",
version="12b.5858"
),
"Export": dict(
export_id="niiri:export_id",
label="NIDM-Results export",
exporter_id="niiri:exporter_id"
)
}
NIDM_SPM_DIR = os.path.join(os.path.dirname(
os.path.dirname(os.path.abspath(__file__))), 'spm', "example001")
ttl_file = os.path.join(NIDM_SPM_DIR, 'example001_spm_results.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def main():
nidm_classes = {
"DesignMatrix": dict(
design_matrix_id='niiri:design_matrix_id',
label="Design Matrix",
location="file:///path/to/DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id"),
"Image-DesignMatrix": dict(
image_id="niiri:design_matrix_png_id",
location="file:///path/to/DesignMatrix.png",
filename="DesignMatrix.png",
format="image/png"
),
"Data": dict(
data_id='niiri:data_id',
label="Data",
scaling="true",
target=100
),
"ErrorModel": dict(
error_model_id="niiri:error_model_id",
noise_distribution="obo:STATO_0000227",
variance_homo="true",
variance_spatial="nidm:NIDM_0000073",
dependence="nidm:NIDM_0000048",
dependence_spatial="nidm:NIDM_0000073"
),
"MaskMap-1": dict( # Explicit mask used by Model Param. Est.
mask_id="niiri:mask_id_1",
label="Mask Map 1",
location="file:///path/to/Mask_1.nii.gz",
filename="Mask_1.nii.gz",
user_defined="true",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
used_by_act_id="niiri:model_pe_id"
),
"DerivedMap-MaskMap-1": dict(
derived_from_map_id="niiri:mask_id_1_der",
derived_map_type="nidm:NIDM_0000054",
filename="MaskMap_1_der.nii",
format="image/nifti",
sha="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:mask_id_1"
),
"ModelParametersEstimation": dict(
model_pe_id="niiri:model_pe_id",
label="Model parameters estimation",
est_method=STATO_OLS_STR,
est_method_comment=STATO_OLS_LABEL,
design_matrix_id="niiri:design_matrix_id",
data_matrix_id="niiri:data_id",
error_model_id="niiri:error_model_id",
software_id="niiri:software_id"
),
"ParameterEstimateMap_Location-1": dict(
beta_map_id="niiri:beta_map_id_1",
label="Beta Map 1",
location="file:///path/to/ParameterEstimate_0001.nii.gz",
filename="ParameterEstimate_0001.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_pe_id"),
"DerivedMapWithHeader-PE1": dict(
derived_from_map_id="niiri:beta_map_id_1_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0001.img",
format="image/nifti",
derived_from_map_header_id="niiri:original_pe_map_header_id",
sha="e43b6e01b0463fe7d40782137867a...",
format_header="image/nifti",
filename_header="beta_0001.hdr",
sha_header="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:beta_map_id_1"
),
"ParameterEstimateMap_Location-2": dict(
beta_map_id="niiri:beta_map_id_2",
label="Beta Map 2",
location="file:///path/to/ParameterEstimate_0002.nii",
filename="ParameterEstimate_0002.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_pe_id"),
"CoordinateSpace-1": dict(
coordinate_space_id="niiri:coordinate_space_id_1",
label="Coordinate space 1",
voxel_to_world_mapping=
"[[-3, 0, 0, 78],[0, 3, 0, -112],[0, 0, 3, -50],[0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000051",
number_of_dim="3",
dimensions="[ 53, 63, 46 ]"),
"ResidualMeanSquaresMap": dict(
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
label="Residual Mean Squares Map",
location="file:///path/to/ResidualMeanSquares.nii.gz",
filename="ResidualMeanSquares.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_pe_id"),
"MaskMap_Analysis": dict( # Mask generated by Model Param. Est.
# (analysis mask)
mask_id="niiri:mask_id_2",
label="Mask Map 2",
location="file:///path/to/Mask.nii.gz",
filename="Mask.nii.gz",
user_defined="false",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
generated_by_act_id="niiri:model_pe_id",
used_by_act_id="niiri:contrast_estimation_id"),
"DerivedMapWithHeader-Mask2": dict(
derived_from_map_id="niiri:mask_id_2_der",
derived_map_type="nidm:NIDM_0000054",
filename="mask.img",
format="image/nifti",
derived_from_map_header_id="niiri:original_mask_map_header_id",
sha="e43b6e01b0463fe7d40782137867a...",
format_header="image/nifti",
filename_header="mask.hdr",
sha_header="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:mask_id_2"
),
"ContrastWeights": dict(
contrast_id="niiri:contrast_id",
label="Contrast: Listening > Rest",
value="[ 1, 0, 0 ]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > rest"
),
"ContrastEstimation": dict(
contrast_estimation_id="niiri:contrast_estimation_id",
label="Contrast estimation",
software_id="niiri:software_id",
mask_id="niiri:mask_id_2",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id",
param_est_map="niiri:beta_map_id_1"
),
"ContrastEstUsedParamEst-Con1PE2": dict(
contrast_estimation_id="niiri:contrast_estimation_id",
param_est_map="niiri:beta_map_id_2"
),
"ContrastMap": dict(
contrast_map_id="niiri:contrast_map_id",
label="Contrast Map: listening > rest",
location="file:///path/to/Contrast.nii.gz",
format="image/nifti",
filename="Contrast.nii.gz",
contrast_name="listening > rest",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
contrast_est_id="niiri:contrast_estimation_id"),
"ContrastStandardErrorMap": dict(
contrast_standard_error_map_id=
"niiri:contrast_standard_error_map_id",
label="Contrast Standard Error Map",
location="file:///path/to/ContrastStandardError.nii.gz",
format="image/nifti",
filename="ContrastStandardError.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
contrast_est_id="niiri:contrast_estimation_id"),
"StatisticMap_T": dict(
statistic_map_id="niiri:statistic_map_id",
label="Statistic Map: listening > rest",
location="file:///path/to/TStatistic.nii.gz",
format="image/nifti",
filename="TStatistic.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > rest",
error_dof="72.9999999990787",
effect_dof="1",
sha="e43b6e01b0463fe7d40782137867a...",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id"),
"DerivedMapWithHeader-StatMap": dict(
derived_from_map_id="niiri:statistic_map_id_der",
derived_map_type="nidm:NIDM_0000076",
filename="spmT_0001.img",
format="image/nifti",
derived_from_map_header_id=
"niiri:statistic_original_map_header_id",
sha="e43b6e01b0463fe7d40782137867a...",
format_header="image/nifti",
filename_header="spmT_0001.hdr",
sha_header="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:statistic_map_id"
),
"HeightThreshold_equivThresh_equivThresh2": dict(
height_threshold_id="niiri:height_threshold_id",
thresh_type=OBO_P_VALUE_FWER_QNAME,
label="Height Threshold: p<0.05 (FWE)",
value="0.05",
equiv_thresh="niiri:height_threshold_id_2",
equiv_thresh2="niiri:height_threshold_id_3"
),
"HeightThreshold-2": dict(
height_threshold_id="niiri:height_threshold_id_2",
thresh_type=OBO_STATISTIC_QNAME,
label="Height Threshold: p<5.23529984739211",
value="5.23529984739211"
),
"HeightThreshold-3": dict(
height_threshold_id="niiri:height_threshold_id_3",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
label="Height Threshold: p<7.62276079258051e-07 (uncorrected)",
value="7.62276079258051e-07",
),
"ExtentThresholdStat_equivThresh_equivThresh2_clusterSizeResels": dict(
extent_threshold_id="niiri:extent_threshold_id",
label="Extent Threshold: k>=0",
cluster_size_vox="0",
cluster_size_resels="0",
equiv_thresh="niiri:height_threshold_id_2",
equiv_thresh2="niiri:height_threshold_id_3"
),
"ExtentThreshold-2": dict(
extent_threshold_id="niiri:extent_threshold_id_2",
label="Extent Threshold",
thresh_type=OBO_P_VALUE_FWER_QNAME,
value="1",
),
"ExtentThreshold-3": dict(
extent_threshold_id="niiri:extent_threshold_id_3",
label="Extent Threshold",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
value="1",
),
"DisplayMaskMap": dict(
display_map_id="niiri:display_map_id",
label="Display Mask Map",
location="file:///path/to/DisplayMask.nii.gz",
format="image/nifti",
user_defined="true",
filename="DisplayMask.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_2",
sha="e43b6e01b0463fe7d40782137867a..."
),
"PeakDefinitionCriteria_MaxPeaks": dict(
peak_definition_criteria_id="niiri:peak_definition_criteria_id",
label="Peak Definition Criteria",
max_num_peaks="3",
min_dist_peaks="8.0"
),
"ClusterDefinitionCriteria": dict(
cluster_definition_criteria_id=
"niiri:cluster_definition_criteria_id",
label="Cluster Connectivity Criterion: 18",
connectivity="nidm:NIDM_0000128"
),
"MaskMap-2": dict( # Explicit mask used by Inference
mask_id="niiri:mask_id_3",
label="Mask Map",
location="file:///path/to/Mask_3.nii.gz",
filename="Mask_3.nii.gz",
user_defined="true",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_2",
sha="e43b6e01b0463fe7d40782137867a...",
used_by_act_id="niiri:inference_id"
),
"CoordinateSpace-2": dict(
coordinate_space_id="niiri:coordinate_space_id_2",
label="Coordinate space 2",
voxel_to_world_mapping=
"[[-3, 0, 0, 78],[0, 3, 0, -112],[0, 0, 3, -50],[0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000051",
number_of_dim="3",
dimensions="[ 53, 63, 46 ]"),
"Inference": dict(
inference_id="niiri:inference_id",
label="Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id="niiri:statistic_map_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
display_mask_id="niiri:display_map_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_2",
software_id="niiri:software_id"
),
"ExcursionSetMap": dict(
id="niiri:excursion_set_map_id",
label="Excursion Set Map",
location="file:///path/to/ExcursionSet.nii.gz",
format="image/nifti",
filename="ExcursionSet.nii.gz",
cluster_label_map_id="niiri:cluster_label_map_id",
max_intensity_projection_id=
"niiri:maximum_intensity_projection_id",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
num_of_clusters="8",
p_value="8.95949980872501e-14",
inference_id="niiri:inference_id"
),
"SignificantCluster-1": dict(
cluster_id="niiri:significant_cluster_0001",
label="Significant Cluster 0001",
cluster_size_in_voxels="530",
cluster_label_id="1",
cluster_size_in_resels="23.1209189500945",
p_value_unc="9.56276736481136e-52",
p_value_fwe="0",
p_value_fdr="7.65021389184909e-51",
excursion_set_id="niiri:excursion_set_map_id"
),
"SignificantCluster-2": dict(
cluster_id="niiri:significant_cluster_0002",
label="Significant Cluster 0002",
cluster_size_in_voxels="445",
cluster_label_id="2",
cluster_size_in_resels="19.4128470430038",
p_value_unc="3.91543427861809e-46",
p_value_fwe="0",
p_value_fdr="1.56617371144723e-45",
excursion_set_id="niiri:excursion_set_map_id"
),
"SignificantCluster-3": dict(
cluster_id="niiri:significant_cluster_0003",
label="Significant Cluster 0003",
cluster_size_in_voxels="38",
cluster_label_id="3",
cluster_size_in_resels="1.6577262643464",
p_value_unc="1.56592642027122e-09",
p_value_fwe="1.39237954499549e-10",
p_value_fdr="4.17580378738993e-09",
excursion_set_id="niiri:excursion_set_map_id"
),
"Peak_ValueP-1": dict(
peak_id="niiri:peak_0001",
label="Peak 0001",
location="niiri:coordinate_0001",
value="13.9346199035645",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="6.3705194444993e-11",
cluster_id="niiri:significant_cluster_0001"
),
"Coordinate-1": dict(
coordinate_id="niiri:coordinate_0001",
label="Coordinate: 0001",
coord="[ -60, -28, 13 ]"
),
"Peak_ValueP-2": dict(
peak_id="niiri:peak_0002",
label="Peak 0002",
location="niiri:coordinate_0002",
value="11.3457498550415",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="3.12855975726156e-10",
cluster_id="niiri:significant_cluster_0001"
),
"Coordinate-2": dict(
coordinate_id="niiri:coordinate_0002",
label="Coordinate: 0002",
coord="[ -66, -13, 4 ]"
),
"Peak_ValueP-3": dict(
peak_id="niiri:peak_0003",
label="Peak 0003",
location="niiri:coordinate_0003",
value="9.82185649871826",
equiv_z="7.80404869241187",
p_uncorr="2.99760216648792e-15",
p_value_fwe="1.82057147135595e-10",
p_value_fdr="9.95383070867767e-08",
cluster_id="niiri:significant_cluster_0001"
),
"Coordinate-3": dict(
coordinate_id="niiri:coordinate_0003",
label="Coordinate: 0003",
coord="[ -63, -7, -2 ]"
),
"Peak_ValueP-4": dict(
peak_id="niiri:peak_0004",
label="Peak 0004",
location="niiri:coordinate_0004",
value="13.7208814620972",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="6.3705194444993e-11",
cluster_id="niiri:significant_cluster_0002"
),
"Coordinate-4": dict(
coordinate_id="niiri:coordinate_0004",
label="Coordinate: 0004",
coord="[ 57, -22, 13 ]"
),
"Peak_ValueP-5": dict(
peak_id="niiri:peak_0005",
label="Peak 0005",
location="niiri:coordinate_0005",
value="12.322901725769",
equiv_z="INF",
p_uncorr="4.44089209850063e-16",
p_value_fwe="0",
p_value_fdr="6.3705194444993e-11",
cluster_id="niiri:significant_cluster_0002"
),
"Coordinate-5": dict(
coordinate_id="niiri:coordinate_0005",
label="Coordinate: 0005",
coord="[ 66, -13, -2 ]"
),
"Peak_ValueP-6": dict(
peak_id="niiri:peak_0006",
label="Peak 0006",
location="niiri:coordinate_0006",
value="9.62070846557617",
equiv_z="7.7026943536333",
p_uncorr="6.66133814775094e-15",
p_value_fwe="4.2237258135458e-10",
p_value_fdr="1.58195372181651e-07",
cluster_id="niiri:significant_cluster_0002"
),
"Coordinate-6": dict(
coordinate_id="niiri:coordinate_0006",
label="Coordinate: 0006",
coord="[ 57, -40, 7 ]"
),
"Peak_ValueP-7": dict(
peak_id="niiri:peak_0007",
label="Peak 0007",
location="niiri:coordinate_0007",
value="7.49709033966064",
equiv_z="6.43494304364426",
p_uncorr="6.17598194807556e-11",
p_value_fwe="4.05099727462943e-06",
p_value_fdr="0.000463130517859672",
cluster_id="niiri:significant_cluster_0003"
),
"Coordinate-7": dict(
coordinate_id="niiri:coordinate_0007",
label="Coordinate: 0007",
coord="[ 36, -31, -14 ]"
),
"SearchSpaceMaskMap": dict(
search_space_id="niiri:search_space_mask_id",
location="file:///path/to/SearchSpaceMask.nii.gz",
filename="SearchSpaceMask.nii.gz",
label="Search Space Mask Map",
format="image/nifti",
user_defined="false",
coordinate_space_id="niiri:coordinate_space_id_2",
expected_num_voxels="0.553331387916112",
expected_num_clusters="0.0889172687960151",
height_critical_fwe05="5.23529984739211",
height_critical_fdr05="6.22537899017334",
smallest_size_fwe05="1",
smallest_size_fdr05="3",
search_vol_voxels="65593",
search_vol_units="1771011",
resel_size="22.9229643140043",
search_vol_resels="2552.68032521656",
search_vol_resels_geom=
"[3, 72.3216126440484, 850.716735116472, 2552.68032521656]",
noise_fwhm_in_voxels=
"[ 2.95881189165801, 2.96628446669584, 2.61180425626264 ]",
noise_fwhm_in_units=
"[ 8.87643567497404, 8.89885340008753, 7.83541276878791 ]",
random_field_station="false",
sha="e43b6e01b0463fe7d40782137867a...",
inference_id="niiri:inference_id"
),
"DerivedMapWithHeader": dict(
derived_from_map_id="niiri:contrast_map_id_der",
derived_map_type="nidm:NIDM_0000002",
filename="con_0001.img",
format="image/nifti",
derived_from_map_header_id="niiri:original_contrast_map_header_id",
sha="e43b6e01b0463fe7d40782137867a...",
format_header="image/nifti",
filename_header="con_0001.hdr",
sha_header="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:contrast_map_id"
),
"DerivedMapWithHeader-2": dict(
derived_from_map_id="niiri:beta_map_id_2_der",
derived_map_type="nidm:NIDM_0000061",
filename="beta_0002.img",
format="image/nifti",
derived_from_map_header_id="niiri:original_pe_map_header_2_id",
sha="e43b6e01b0463fe7d40782137867a...",
format_header="image/nifti",
filename_header="beta_0002.hdr",
sha_header="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:beta_map_id_2"
),
"DerivedMapWithHeader-3": dict(
derived_from_map_id="niiri:statistic_map_id_der",
derived_map_type="nidm:NIDM_0000076",
filename="spmT_0001.img",
format="image/nifti",
derived_from_map_header_id=
"niiri:statistic_original_map_header_id",
sha="e43b6e01b0463fe7d40782137867a...",
format_header="image/nifti",
filename_header="spmT_0001.hdr",
sha_header="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:statistic_map_id"
),
"NIDMBundle": dict(
bundle_id="niiri:spm_results_id",
label="NIDM-Results",
object_model="nidm:NIDM_0000027",
version="1.1.0",
time="2014-05-19T10:30:00.000+01:00"
),
"SPM_ReselsPerVoxelMap": dict(
resels_per_voxel_map_id="niiri:resels_per_voxel_map_id",
label="Resels per Voxel Map",
location="file:///path/to/ReselsPerVoxel.nii.gz",
filename="ReselsPerVoxel.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
model_pe_id="niiri:model_pe_id"
),
"SPM_InferenceUsedRPVMap": dict(
inference_id="niiri:inference_id",
resels_per_voxel_map_id="niiri:resels_per_voxel_map_id"
),
"DerivedMapWithHeader-4": dict(
derived_from_map_id="niiri:resels_per_voxel_map_id_der",
derived_map_type="nidm:NIDM_0000144",
filename="RPV.img",
format="image/nifti",
derived_from_map_header_id="niiri:original_rpv_map_header_id",
sha="e43b6e01b0463fe7d40782137867a...",
format_header="image/nifti",
filename_header="RPV.hdr",
sha_header="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:resels_per_voxel_map_id"
),
"ClusterLabelsMap": dict(
cluster_label_map_id="niiri:cluster_label_map_id",
location="file:///path/to/ClusterLabels.nii.gz",
filename="ClusterLabels.nii.gz",
format="image/nifti"
),
"SPM_Software": dict(
software_id="niiri:software_id",
software_type="nlx:nif-0000-00343",
label="SPM",
version="12b.5853"
),
"Image": dict(
image_id="niiri:maximum_intensity_projection_id",
location="file:///path/to/MaximumIntensityProjection.png",
filename="MaximumIntensityProjection.png",
format="image/png"
),
"GrandMeanMap": dict(
grand_mean_map_id="niiri:grand_mean_map_id",
label="Grand Mean Map",
location="file:///path/to/GrandMean.nii.gz",
filename="GrandMean.nii.gz",
format="image/nifti",
masked_median="115",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
model_pe_id="niiri:model_pe_id"
)
}
NIDM_SPM_DIR = os.path.join(os.path.dirname(
os.path.dirname(os.path.abspath(__file__))), 'spm')
ttl_file = os.path.join(NIDM_SPM_DIR, 'spm_results.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
def main():
nidm_classes = {
"DesignMatrix": dict(
design_matrix_id='niiri:design_matrix_id',
label="Design Matrix",
location="file://path/to/DesignMatrix.csv",
format="text/csv",
filename="DesignMatrix.csv",
design_matrix_png_id="niiri:design_matrix_png_id"),
"Image-DesignMatrix": dict(
image_id="niiri:design_matrix_png_id",
location="file://path/to/DesignMatrix.png",
filename="DesignMatrix.png",
format="image/png"
),
"Data": dict(
data_id='niiri:data_id',
label="Data",
scaling="true",
target="10000"
),
"ErrorModel": dict(
error_model_id="niiri:error_model_id",
noise_distribution="nidm:NIDM_0000032",
variance_homo="true",
variance_spatial="nidm:NIDM_0000073",
dependence="nidm:NIDM_0000048",
dependence_spatial="nidm:NIDM_0000073"
),
"ModelParametersEstimation": dict(
model_pe_id="niiri:model_pe_id",
label="Model parameters estimation",
est_method=STATO_OLS_STR,
est_method_comment=STATO_OLS_LABEL,
design_matrix_id="niiri:design_matrix_id",
data_matrix_id="niiri:data_id",
error_model_id="niiri:error_model_id",
software_id="niiri:software_id"
),
"FSL_ParameterEstimateMap-1": dict(
beta_map_id="niiri:beta_map_id_1",
label="Parameter estimate 1",
location="file://path/to/ParameterEstimate_0001.nii.gz",
filename_1="pe1.nii.gz",
filename_2="ParameterEstimate_0001.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="f51b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_pe_id"),
"FSL_ParameterEstimateMap-2": dict(
beta_map_id="niiri:beta_map_id_2",
label="Parameter estimate 2",
location="file://path/to/ParameterEstimate_0002.nii.gz",
filename_1="pe2.nii.gz",
filename_2="ParameterEstimate_0002.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="p89b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_pe_id"),
"CoordinateSpace-1": dict(
coordinate_space_id="niiri:coordinate_space_id_1",
label="Coordinate space 1",
voxel_to_world_mapping="[[-3, 0, 0, 81],[0, 3, 0, -115],[0, 0, 3, -53],[0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000047",
number_of_dim="3",
dimensions="[ 53, 63, 46 ]"),
"CoordinateSpace-2": dict(
coordinate_space_id="niiri:coordinate_space_id_2",
label="Coordinate space 2",
voxel_to_world_mapping="[[-3, 0, 0, 81],[0, 3, 0, -115],[0, 0, 3, -53],[0, 0, 0, 1]]",
voxel_units="[ \\\"mm\\\", \\\"mm\\\", \\\"mm\\\" ]",
voxel_size="[ 3, 3, 3 ]",
coord_system="nidm:NIDM_0000047",
number_of_dim="3",
dimensions="[ 53, 63, 46 ]"),
"FSL_ResidualMeanSquaresMap": dict(
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
label="Residual Mean Squares Map",
location="file://path/to/ResidualMeanSquares.nii.gz",
filename_1="ResidualMeanSquares.nii.gz",
filename_2="sigmasquareds.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
param_est_id="niiri:model_pe_id"),
"MaskMap_Analysis_fileName": dict( # The analysis mask
mask_id="niiri:mask_id_1",
label="Mask",
location="file://path/to/Mask.nii.gz",
filename="Mask.nii.gz",
filename_2="mask.nii.gz",
user_defined="false",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
generated_by_act_id="niiri:model_pe_id",
used_by_act_id="niiri:contrast_estimation_id"),
"ContrastWeights": dict(
contrast_id="niiri:contrast_id",
label="Contrast weights: listening > rest",
value="[ 1, 0, 0 ]",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > rest"
),
"ContrastEstimation": dict(
contrast_estimation_id="niiri:contrast_estimation_id",
label="Contrast estimation",
software_id="niiri:software_id",
mask_id="niiri:mask_id_1",
residual_mean_squares_map_id="niiri:residual_mean_squares_map_id",
design_matrix_id="niiri:design_matrix_id",
contrast_id="niiri:contrast_id",
param_est_map="niiri:beta_map_id_1"
),
"ContrastEstUsedParamEst-1-2": dict(
contrast_estimation_id="niiri:contrast_estimation_id",
param_est_map="niiri:beta_map_id_2"
),
"FSL_ContrastMap": dict(
contrast_map_id="niiri:contrast_map_id",
label="Contrast Map: listening > rest",
location="file://path/to/Contrast.nii.gz",
format="image/nifti",
filename_1="Contrast.nii.gz",
filename_2="cope1.nii.gz",
contrast_name="listening > rest",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="400a2f07d99ed9be06577e6ecc89222cf4b688c654bc89067da558e88b73b97dd1b25e6c98f2a735fa0a1409598cff7e6025bda55abb6b9f5ef65d8d307eeba8",
contrast_est_id="niiri:contrast_estimation_id"),
"ContrastStandardErrorMap": dict(
contrast_standard_error_map_id="niiri:contrast_standard_error_map_id",
label="Contrast Standard Error Map",
location="file://path/to/ContrastStandardError.nii.gz",
format="image/nifti",
filename="ContrastStandardError.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
contrast_est_id="niiri:contrast_estimation_id"),
"FSL_DerivedMap-ContrastVariance": dict(
derived_from_map_id="niiri:contrast_variance_map_id",
derived_map_type="nidm:NIDM_0000135",
filename="varcope1.nii.gz",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
map_id="niiri:contrast_standard_error_map_id"
),
"FSL_StatisticMap": dict(
statistic_map_id="niiri:statistic_map_id",
label="Statistic Map: listening > rest",
location="file://path/to/TStatistic_0001.nii.gz",
format="image/nifti",
filename_1="TStatistic_0001.nii.gz",
filename_2="tstat1.nii.gz",
statistic_type=STATO_TSTATISTIC_STR,
stat_type_comment=STATO_TSTATISTIC_LABEL,
contrast_name="listening > rest",
error_dof="73.0",
effect_dof="1",
sha="400a2f07d99ed9be06577e6ecc89222cf4b688c654bc89067da558e88b73b97dd1b25e6c98f2a735fa0a1409598cff7e6025bda55abb6b9f5ef65d8d307eeba8",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id"),
"FSL_StatisticMap-Z": dict(
statistic_map_id="niiri:z_statistic_map_id",
label="Z-Statistic Map: listening > rest",
location="file://path/to/ZStatistic_0001.nii.gz",
format="image/nifti",
filename_1="ZStatistic_0001.nii.gz",
filename_2="zstat1.nii.gz",
statistic_type=STATO_ZSTATISTIC_STR,
contrast_name="listening > rest",
error_dof="INF",
effect_dof="1",
sha="400a2f07d99ed9be06577e6ecc89222cf4b688c654bc89067da558e88b73b97dd1b25e6c98f2a735fa0a1409598cff7e6025bda55abb6b9f5ef65d8d307eeba8",
coordinate_space_id="niiri:coordinate_space_id_1",
contrast_est_id="niiri:contrast_estimation_id"),
"HeightThreshold_equivThresh_equivThresh2": dict(
height_threshold_id="niiri:height_threshold_id",
thresh_type=OBO_P_VALUE_FWER_QNAME,
label="Height Threshold: p<0.05 (FWE)",
value="0.05",
equiv_thresh="niiri:height_threshold_id_2",
equiv_thresh2="niiri:height_threshold_id_3"
),
"HeightThreshold-2": dict(
height_threshold_id="niiri:height_threshold_id_2",
thresh_type=OBO_STATISTIC_QNAME,
label="Height Threshold",
value="5.235300"
),
"HeightThreshold-3": dict(
height_threshold_id="niiri:height_threshold_id_3",
thresh_type=NIDM_P_VALUE_UNCORRECTED_QNAME,
label="Height Threshold",
value="0.000001",
),
"ExtentThreshold": dict(
extent_threshold_id="niiri:extent_threshold_id",
label="Cluster Threshold",
thresh_type=OBO_P_VALUE_FWER_QNAME,
value="1",
),
"DisplayMaskMap_fileName": dict(
display_map_id="niiri:display_map_id",
label="Display Mask Map",
location="file://path/to/DisplayMask.nii.gz",
format="image/nifti",
user_defined="true",
filename="DisplayMask.nii.gz",
filename_2="mask.nii.gz",
coordinate_space_id="niiri:coordinate_space_id_2",
sha="e43b6e01b0463fe7d40782137867a..."
),
"PeakDefinitionCriteria_MaxPeaks": dict(
peak_definition_criteria_id="niiri:peak_definition_criteria_id",
label="Peak Definition Criteria",
max_num_peaks="3",
min_dist_peaks="8.0"
),
"ClusterDefinitionCriteria": dict(
cluster_definition_criteria_id="niiri:cluster_definition_criteria_id",
label="Cluster Connectivity Criterion: 18",
connectivity="nidm:NIDM_0000128"
),
"Inference": dict(
inference_id="niiri:inference_id",
label="Inference",
alternative_hyp="nidm:NIDM_0000060",
stat_map_id="niiri:z_statistic_map_id",
height_thresh_id="niiri:height_threshold_id",
extent_thresh_id="niiri:extent_threshold_id",
display_mask_id="niiri:display_map_id",
peak_def_id="niiri:peak_definition_criteria_id",
cluster_def_id="niiri:cluster_definition_criteria_id",
mask_id="niiri:mask_id_1",
software_id="niiri:software_id"
),
"FSL_ExcursionSetMap": dict(
id="niiri:excursion_set_map_id",
label="Excursion Set Map",
location="file://path/to/ExcursionSet.nii.gz",
format="image/nifti",
filename_1="ExcursionSet.nii.gz",
filename_2="thresh_zstat1.nii.gz",
cluster_label_map_id="niiri:cluster_label_map_id",
png_id="niiri:excursion_set_png_id_1",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="400a2f07d99ed9be06577e6ecc89222cf4b688c654bc89067da558e88b73b97dd1b25e6c98f2a735fa0a1409598cff7e6025bda55abb6b9f5ef65d8d307eeba8",
inference_id="niiri:inference_id"
),
"Image": dict(
image_id="niiri:excursion_set_png_id_1",
location="file://path/to/rendered_thresh_zstat1.png",
filename="rendered_thresh_zstat1.png",
format="image/png"
),
"FSL_SignificantCluster-1": dict(
cluster_id="niiri:significant_cluster_0001",
label="Significant Cluster 0001",
cluster_size_in_voxels="530",
cluster_label_id="1",
p_value_fwe="0.000000",
excursion_set_id="niiri:excursion_set_map_id"
),
"FSL_ClusterCenterOfGravity-1": dict(
center_of_gravity_id="niiri:center_of_gravity_1",
label="Center of gravity 1",
location="niiri:COG_coordinate_0001",
cluster_id="niiri:significant_cluster_0001"
),
"FSL_Coordinate-COG1": dict(
coordinate_id="niiri:COG_coordinate_0001",
label="Coordinate 1",
coord="[ 40.2, 16.4, 13.2 ]",
coord_in_vox="[ -30.8, -68.5, -13.4 ]",
),
"FSL_SignificantCluster-2": dict(
cluster_id="niiri:significant_cluster_0002",
label="Significant Cluster 0002",
cluster_size_in_voxels="445",
cluster_label_id="2",
p_value_fwe="0.000000",
excursion_set_id="niiri:excursion_set_map_id"
),
"FSL_ClusterCenterOfGravity-2": dict(
center_of_gravity_id="niiri:center_of_gravity_2",
label="Center of gravity 2",
location="niiri:COG_coordinate_0002",
cluster_id="niiri:significant_cluster_0002"
),
"FSL_Coordinate-COG2": dict(
coordinate_id="niiri:COG_coordinate_0002",
label="Coordinate 2",
coord="[ 25.6, 12.8, 14.6 ]",
coord_in_vox="[ 24.1, -77.1, -4.27 ]"
),
"Peak-M1": dict(
peak_id="niiri:peak_0001",
label="Peak 1",
p_uncorr="4.126074e-10",
location="niiri:coordinate_0001",
equiv_z="6.14",
cluster_id="niiri:significant_cluster_0001"
),
"FSL_Coordinate-1": dict(
coordinate_id="niiri:coordinate_0001",
label="Coordinate 1",
coord="[ -48.1, -73.7, -9.24 ]",
coord_in_vox="[ 45, 15, 14 ]",
),
"Peak-2": dict(
peak_id="niiri:peak_0002",
label="Peak 2",
p_uncorr="7.705712e-10",
location="niiri:coordinate_0002",
equiv_z="6.04",
cluster_id="niiri:significant_cluster_0001"
),
"FSL_Coordinate-2": dict(
coordinate_id="niiri:coordinate_0002",
label="Coordinate 2",
coord="[ -38.1, -53.4, -18 ]",
coord_in_vox="[ 42, 21, 13 ]",
),
"Peak-3": dict(
peak_id="niiri:peak_0003",
label="Peak 3",
p_uncorr="4.462172e-09",
location="niiri:coordinate_0003",
equiv_z="5.75",
cluster_id="niiri:significant_cluster_0001"
),
"FSL_Coordinate-3": dict(
coordinate_id="niiri:coordinate_0003",
label="Coordinate 3",
coord="[ -29.6, -73.8, -16.9 ]",
coord_in_vox="[ 40, 15, 12 ]",
),
"Peak-4": dict(
peak_id="niiri:peak_0004",
label="Peak 4",
p_uncorr="4.462172e-09",
location="niiri:coordinate_0004",
equiv_z="5.75",
cluster_id="niiri:significant_cluster_0001"
),
"FSL_Coordinate-4": dict(
coordinate_id="niiri:coordinate_0004",
label="Coordinate 4",
coord="[ 0.791, -87.2, 3.23 ]",
coord_in_vox="[ 39, 13, 12 ]"
),
"Peak-M5": dict(
peak_id="niiri:peak_0005",
label="Peak 5",
p_uncorr="2.178976e-09",
location="niiri:coordinate_0005",
equiv_z="5.87",
cluster_id="niiri:significant_cluster_0002"
),
"FSL_Coordinate-5": dict(
coordinate_id="niiri:coordinate_0005",
label="Coordinate 5",
coord="[ 16.1, -96.6, 5.82 ]",
coord_in_vox="[ 32, 10, 16 ]"
),
"Peak-6": dict(
peak_id="niiri:peak_0006",
label="Peak 6",
p_uncorr="8.022392e-09",
location="niiri:coordinate_0006",
equiv_z="5.65",
cluster_id="niiri:significant_cluster_0002"
),
"FSL_Coordinate-6": dict(
coordinate_id="niiri:coordinate_0006",
label="Coordinate 6",
coord="[ -25.5, -80.4, 15.3 ]",
coord_in_vox="[ 28, 7, 16 ]"
),
"FSL_SearchSpaceMaskMap": dict(
search_space_id="niiri:search_space_mask_id",
location="file://path/to/SearchSpaceMask.nii.gz",
filename_1="SearchSpaceMask.nii.gz",
filename_2="mask.nii.gz",
label="Search Space Mask Map",
user_defined="false",
format="image/nifti",
coordinate_space_id="niiri:coordinate_space_id_2",
search_vol_voxels="45359",
search_vol_units="1.93808e+06",
search_vol_resels="3753.84",
resel_size="12.2251",
noise_roughness="0.384676",
random_field_station="true",
sha="400a2f07d99ed9be06577e6ecc89222cf4b688c654bc89067da558e88b73b97dd1b25e6c98f2a735fa0a1409598cff7e6025bda55abb6b9f5ef65d8d307eeba8",
inference_id="niiri:inference_id",
noise_fwhm_in_voxels="[2.38803, 2.43263, 2.07288]",
noise_fwhm_in_units="[8.35811, 8.5142, 7.2551]"
),
"NIDMBundle": dict(
bundle_id="niiri:fsl_results_id",
label="NIDM-Results",
object_model="nidm:NIDM_0000027",
version="1.1.0",
time="2014-05-19T10:30:00.000+01:00"
),
"FSL_Software": dict(
software_id="niiri:software_id",
software_type="nlx:birnlex_2067",
label="FSL",
version="5.0.x",
feat_version="6.00"
),
"FSL_GrandMeanMap": dict(
grand_mean_map_id="niiri:grand_mean_map_id",
label="Grand Mean Map",
location="file://path/to/GrandMean.nii.gz",
filename_1="GrandMean.nii.gz",
filename_2="mean_func.nii.gz",
format="image/nifti",
masked_median="115",
coordinate_space_id="niiri:coordinate_space_id_1",
sha="e43b6e01b0463fe7d40782137867a...",
model_pe_id="niiri:model_pe_id"
)
}
NIDM_FSL_DIR = os.path.join(os.path.dirname(
os.path.dirname(os.path.abspath(__file__))), 'fsl')
ttl_file = os.path.join(NIDM_FSL_DIR, 'fsl_results.ttl')
example = ExampleFromTemplate(nidm_classes, ttl_file, False)
example.create_example()
