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 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 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 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 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 = { "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_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 = { "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": 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="1.3.0", 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 = { "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" ), "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="scr:SCR_007037", 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": 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" ), "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="10000", scanner_id="niiri:mr_scanner_id", sub_or_group_id="niiri:group_id", group2_id="niiri:group2_id", mri_protocol=NLX_FMRI_PROTOCOL, 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-1": dict( beta_map_id="niiri:beta_map_id_1", label="Parameter estimate 1", location="file://path/to/ParameterEstimate_001.nii.gz", filename="ParameterEstimate_001.nii.gz", format="image/nifti", coordinate_space_id="niiri:coordinate_space_id_1", sha="f51b6e01b0463fe7d40782137867a", param_est_id="niiri:model_pe_id"), "ParameterEstimateMap-2": dict( beta_map_id="niiri:beta_map_id_2", label="Parameter estimate 2", location="file://path/to/ParameterEstimate_002.nii.gz", filename="ParameterEstimate_002.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="400a2f07d99ed9be06577e6ecc89222cf4b688c654bc89067da558e88b73b\ 97dd1b25e6c98f2a735fa0a1409598cff7e6025bda55abb6b9f5ef65d8d307eeba8", 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="T-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="400a2f07d99ed9be06577e6ecc89222cf4b688c654bc89067da558e88b73b\ 97dd1b25e6c98f2a735fa0a1409598cff7e6025bda55abb6b9f5ef65d8d307eeba8", 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="400a2f07d99ed9be06577e6ecc89222cf4b688c654bc89067da558e88b73b\ 97dd1b25e6c98f2a735fa0a1409598cff7e6025bda55abb6b9f5ef65d8d307eeba8", 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="400a2f07d99ed9be06577e6ecc89222cf4b688c654bc89067da558e88b73b\ 97dd1b25e6c98f2a735fa0a1409598cff7e6025bda55abb6b9f5ef65d8d307eeba8", 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="400a2f07d99ed9be06577e6ecc89222cf4b688c654bc89067da558e88b73b\ 97dd1b25e6c98f2a735fa0a1409598cff7e6025bda55abb6b9f5ef65d8d307eeba8", 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="1.3.0", 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" ), "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 = { "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="Parameter Estimate Map 1", coordinate_space_id="niiri:coordinate_space_id_1", filename="ParameterEstimate_0001.nii.gz", location="ParameterEstimate_0001.nii.gz", format="image/nifti", sha="fab2573099693215bac756bc796fbc983524473dec5c1b2d66fb83694c174\ 12731df7f574094cb6c4a77994af7be11ed9aa545090fbe8ec6565a5c3c3dae8f0f", param_est_id="niiri:model_pe_id"), "ParameterEstimateMap-2": dict( beta_map_id="niiri:beta_map_id_2", label="Parameter Estimate Map 2", coordinate_space_id="niiri:coordinate_space_id_1", filename="ParameterEstimate_0002.nii.gz", location="ParameterEstimate_0002.nii.gz", format="image/nifti", sha="3f72b788762d9ab2c7ddb5e4d446872694ee42fc8897fe5317b54efb7924f\ 784da6499065db897a49595d8763d1893ad65ad102b0c88f2e72e2d028173343008", param_est_id="niiri:model_pe_id"), "DerivedMap-ParameterEstimateMap-1": 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" ), "DerivedMap-ParameterEstimateMap-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" ), "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_0000050", 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="T-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<0.050000 (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="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" ), "NIDMBundle": dict( bundle_id="niiri:spm_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_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", label="Cluster Labels Map", coordinate_space_id="niiri:coordinate_space_id_1", sha="a132bb284da461fd9e20eb2986373a9171c90a342c1e694297bc02f5674a3\ 11a560b7ff34bdf045dc191d4afff8c690a373db6408c1fe93f7c25e23707ce65c3" ), "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 = { "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"), "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-1": dict(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"), "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-2": dict(beta_map_id="niiri:beta_map_id_2", label="Beta Map 2", location="ParameterEstimate_002.nii", filename="ParameterEstimate_002.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="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"), "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="1.3.0", 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", label="Cluster Labels Map", coordinate_space_id="niiri:coordinate_space_id_1", sha="13093aae03897e2518307d000eb298f4b1439814d8d3d77c622b717423f93\ 506dd5de5669513ab65c6dd74a7d27ee9df08620f546ed00575517b40e5878c2c96"), "SPM_Software": dict(software_id="niiri:software_id", software_type="scr:SCR_007037", 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='[\\\"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()