def test_FitGLM_inputs():
input_map = dict(ignore_exception=dict(nohash=True,
usedefault=True,
),
session_info=dict(mandatory=True,
),
drift_model=dict(usedefault=True,
),
normalize_design_matrix=dict(usedefault=True,
),
TR=dict(mandatory=True,
),
mask=dict(),
save_residuals=dict(usedefault=True,
),
plot_design_matrix=dict(usedefault=True,
),
hrf_model=dict(usedefault=True,
),
model=dict(usedefault=True,
),
method=dict(usedefault=True,
),
)
inputs = FitGLM.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
def test_FitGLM_outputs():
output_map = dict(a=dict(),
nvbeta=dict(),
s2=dict(),
dof=dict(),
beta=dict(),
residuals=dict(),
reg_names=dict(),
constants=dict(),
axis=dict(),
)
outputs = FitGLM.output_spec()
for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value
def test_FitGLM_outputs():
output_map = dict(
a=dict(),
axis=dict(),
beta=dict(),
constants=dict(),
dof=dict(),
nvbeta=dict(),
reg_names=dict(),
residuals=dict(),
s2=dict(),
)
outputs = FitGLM.output_spec()
for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value
def test_FitGLM_inputs():
input_map = dict(
TR=dict(mandatory=True, ),
drift_model=dict(usedefault=True, ),
hrf_model=dict(usedefault=True, ),
ignore_exception=dict(
nohash=True,
usedefault=True,
),
mask=dict(),
method=dict(usedefault=True, ),
model=dict(usedefault=True, ),
normalize_design_matrix=dict(usedefault=True, ),
plot_design_matrix=dict(usedefault=True, ),
save_residuals=dict(usedefault=True, ),
session_info=dict(mandatory=True, ),
)
inputs = FitGLM.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
contrasts = [cont1, cont2]
"""Generate design information using
:class:`nipype.interfaces.spm.SpecifyModel`. nipy accepts only design specified
in seconds so "output_units" has always have to be set to "secs".
"""
modelspec = pe.Node(interface=model.SpecifySPMModel(), name="modelspec")
modelspec.inputs.concatenate_runs = True
modelspec.inputs.input_units = 'secs'
modelspec.inputs.output_units = 'secs'
modelspec.inputs.time_repetition = 3.
modelspec.inputs.high_pass_filter_cutoff = 120
"""Fit the GLM model using nipy and ordinary least square method
"""
model_estimate = pe.Node(interface=FitGLM(), name="model_estimate")
model_estimate.inputs.TR = 3.
model_estimate.inputs.model = "spherical"
model_estimate.inputs.method = "ols"
"""Estimate the contrasts. The format of the contrasts definition is the same as
for FSL and SPM
"""
contrast_estimate = pe.Node(interface=EstimateContrast(),
name="contrast_estimate")
cont1 = ('Task>Baseline', 'T', ['Task-Odd', 'Task-Even'], [0.5, 0.5])
cont2 = ('Task-Odd>Task-Even', 'T', ['Task-Odd', 'Task-Even'], [1, -1])
contrast_estimate.inputs.contrasts = [cont1, cont2]
"""
Setup the pipeline
------------------
def create_model_fit_pipeline(high_pass_filter_cutoff=128,
nipy=False,
ar1=True,
name="model",
save_residuals=False):
inputnode = pe.Node(interface=util.IdentityInterface(fields=[
'outlier_files', "realignment_parameters", "functional_runs", "mask",
'conditions', 'onsets', 'durations', 'TR', 'contrasts', 'units',
'sparse'
]),
name="inputnode")
modelspec = pe.Node(interface=model.SpecifySPMModel(), name="modelspec")
if high_pass_filter_cutoff:
modelspec.inputs.high_pass_filter_cutoff = high_pass_filter_cutoff
create_subject_info = pe.Node(interface=util.Function(
input_names=['conditions', 'onsets', 'durations'],
output_names=['subject_info'],
function=create_subject_inf),
name="create_subject_info")
modelspec.inputs.concatenate_runs = True
#modelspec.inputs.input_units = units
modelspec.inputs.output_units = "secs"
#modelspec.inputs.time_repetition = tr
#modelspec.inputs.subject_info = subjectinfo
model_pipeline = pe.Workflow(name=name)
model_pipeline.connect([
(inputnode, create_subject_info, [('conditions', 'conditions'),
('onsets', 'onsets'),
('durations', 'durations')]),
(inputnode, modelspec, [('realignment_parameters',
'realignment_parameters'),
('functional_runs', 'functional_runs'),
('outlier_files', 'outlier_files'),
('units', 'input_units'),
('TR', 'time_repetition')]),
(create_subject_info, modelspec, [('subject_info', 'subject_info')]),
])
if nipy:
model_estimate = pe.Node(interface=FitGLM(), name="level1estimate")
model_estimate.inputs.TR = tr
model_estimate.inputs.normalize_design_matrix = True
model_estimate.inputs.save_residuals = save_residuals
if ar1:
model_estimate.inputs.model = "ar1"
model_estimate.inputs.method = "kalman"
else:
model_estimate.inputs.model = "spherical"
model_estimate.inputs.method = "ols"
model_pipeline.connect([
(modelspec, model_estimate, [('session_info', 'session_info')]),
(inputnode, model_estimate, [('mask', 'mask')])
])
if contrasts:
contrast_estimate = pe.Node(interface=EstimateContrast(),
name="contrastestimate")
contrast_estimate.inputs.contrasts = contrasts
model_pipeline.connect([
(model_estimate, contrast_estimate,
[("beta", "beta"), ("nvbeta", "nvbeta"), ("s2", "s2"),
("dof", "dof"), ("axis", "axis"), ("constants", "constants"),
("reg_names", "reg_names")]),
(inputnode, contrast_estimate, [('mask', 'mask')]),
])
else:
level1design = pe.Node(interface=spm.Level1Design(),
name="level1design")
level1design.inputs.bases = {'hrf': {'derivs': [0, 0]}}
if ar1:
level1design.inputs.model_serial_correlations = "AR(1)"
else:
level1design.inputs.model_serial_correlations = "none"
level1design.inputs.timing_units = modelspec.inputs.output_units
#level1design.inputs.interscan_interval = modelspec.inputs.time_repetition
# if sparse:
# level1design.inputs.microtime_resolution = n_slices*2
# else:
# level1design.inputs.microtime_resolution = n_slices
#level1design.inputs.microtime_onset = ref_slice
microtime_resolution = pe.Node(interface=util.Function(
input_names=['volume', 'sparse'],
output_names=['microtime_resolution'],
function=_get_microtime_resolution),
name="microtime_resolution")
level1estimate = pe.Node(interface=spm.EstimateModel(),
name="level1estimate")
level1estimate.inputs.estimation_method = {'Classical': 1}
contrastestimate = pe.Node(interface=spm.EstimateContrast(),
name="contrastestimate")
#contrastestimate.inputs.contrasts = contrasts
threshold = pe.MapNode(interface=spm.Threshold(),
name="threshold",
iterfield=['contrast_index', 'stat_image'])
#threshold.inputs.contrast_index = range(1,len(contrasts)+1)
threshold_topo_ggmm = neuroutils.CreateTopoFDRwithGGMM(
"threshold_topo_ggmm")
#threshold_topo_ggmm.inputs.inputnode.contrast_index = range(1,len(contrasts)+1)
model_pipeline.connect([
(modelspec, level1design, [('session_info', 'session_info')]),
(inputnode, level1design, [('mask', 'mask_image'),
('TR', 'interscan_interval'),
(("functional_runs", get_ref_slice),
"microtime_onset")]),
(inputnode, microtime_resolution, [("functional_runs", "volume"),
("sparse", "sparse")]),
(microtime_resolution, level1design, [("microtime_resolution",
"microtime_resolution")]),
(level1design, level1estimate, [('spm_mat_file', 'spm_mat_file')]),
(inputnode, contrastestimate, [('contrasts', 'contrasts')]),
(level1estimate, contrastestimate,
[('spm_mat_file', 'spm_mat_file'), ('beta_images', 'beta_images'),
('residual_image', 'residual_image')]),
(contrastestimate, threshold, [('spm_mat_file', 'spm_mat_file'),
('spmT_images', 'stat_image')]),
(inputnode, threshold, [(('contrasts', _get_contrast_index),
'contrast_index')]),
(level1estimate, threshold_topo_ggmm, [('mask_image',
'inputnode.mask_file')]),
(contrastestimate, threshold_topo_ggmm,
[('spm_mat_file', 'inputnode.spm_mat_file'),
('spmT_images', 'inputnode.stat_image')]),
(inputnode, threshold_topo_ggmm,
[(('contrasts', _get_contrast_index), 'inputnode.contrast_index')
]),
])
return model_pipeline
