def model_fitting(source_img, prepped_img, subject_info, task):
taskdir = os.path.join(outputdir, task)
if not os.path.exists(taskdir):
os.mkdir(taskdir)
# skull strip the preprocessed BOLD
bet = fsl.BET()
bet.inputs.in_file = prepped_img
bet.inputs.frac = 0.7
bet.inputs.functional = True
bet.inputs.out_file = os.path.join(taskdir, task + "_input_functional_bet.nii.gz")
bet_res = bet.run()
bettedinput = bet_res.outputs.out_file
task_vs_baseline = [task + " vs baseline", 'T', [task], [1]] # set up contrasts
contrasts = [task_vs_baseline]
modelfit = pe.Workflow(name='modelfit', base_dir=taskdir) # generate the model fitting workflow
modelspec = pe.Node(interface=model.SpecifyModel(), name="modelspec") # generate design info
level1design = pe.Node(interface=fsl.Level1Design(), name="level1design") # generate fsf file
modelgen = pe.MapNode( # generate .mat file
interface=fsl.FEATModel(),
name='modelgen',
iterfield=['fsf_file', 'ev_files'])
feat = pe.Node( # feat statistics
interface=fsl.FEAT(),
name='feat',
iterfield=['fsf_file'])
# put it all together
modelfit.connect([
(modelspec, level1design, [('session_info', 'session_info')]),
(level1design, modelgen, [('fsf_files', 'fsf_file'), ('ev_files', 'ev_files')]),
(level1design, feat, [('fsf_files', 'fsf_file')])])
# define inputs to workflow
modelspec.inputs.input_units = 'secs'
modelspec.inputs.functional_runs = bettedinput
modelspec.inputs.time_repetition = source_img.entities['RepetitionTime']
modelspec.inputs.high_pass_filter_cutoff = 90
modelspec.inputs.subject_info = subject_info
level1design.inputs.interscan_interval = source_img.entities['RepetitionTime']
level1design.inputs.bases = {'gamma': {'gammasigma': 3, 'gammadelay': 6, 'derivs': True}}
level1design.inputs.contrasts = contrasts
level1design.inputs.model_serial_correlations = True
# Run the model-fitting pipeline. Main outputs are a feat directory (w/ functional img) and a design.mat file
res = modelfit.run()
# outputs
feat_dir = list(res.nodes)[3].result.outputs.feat_dir
thresh_img = feat_dir + "/thresh_zstat1.nii.gz"
return thresh_img
def init_taskbased_wf(
workdir=None,
feature=None,
condition_files=None,
condition_units=None,
memcalc=MemoryCalculator(),
):
"""
create workflow to calculate a first level glm for task functional data
"""
if feature is not None:
name = f"{formatlikebids(feature.name)}_wf"
else:
name = "taskbased_wf"
workflow = pe.Workflow(name=name)
#
inputnode = pe.Node(
niu.IdentityInterface(
fields=[
"tags",
"vals",
"metadata",
"bold",
"mask",
"repetition_time",
"confounds_selected",
"condition_names",
"condition_files",
"condition_units",
]
),
name="inputnode",
)
outputnode = pe.Node(niu.IdentityInterface(fields=["resultdicts"]), name="outputnode")
if feature is not None:
inputnode.inputs.condition_names = feature.conditions
if condition_files is not None:
inputnode.inputs.condition_files = condition_files
if condition_units is not None:
inputnode.inputs.condition_units = condition_units
#
make_resultdicts_a = pe.Node(
MakeResultdicts(tagkeys=["feature"], imagekeys=["design_matrix", "contrast_matrix"]),
name="make_resultdicts_a",
)
if feature is not None:
make_resultdicts_a.inputs.feature = feature.name
workflow.connect(inputnode, "tags", make_resultdicts_a, "tags")
workflow.connect(inputnode, "vals", make_resultdicts_a, "vals")
workflow.connect(inputnode, "metadata", make_resultdicts_a, "metadata")
make_resultdicts_b = pe.Node(
MakeResultdicts(
tagkeys=["feature", "taskcontrast"],
imagekeys=["effect", "variance", "z", "dof", "mask"],
metadatakeys=["sources"],
),
name="make_resultdicts_b",
)
if feature is not None:
make_resultdicts_b.inputs.feature = feature.name
workflow.connect(inputnode, "tags", make_resultdicts_b, "tags")
workflow.connect(inputnode, "vals", make_resultdicts_b, "vals")
workflow.connect(inputnode, "metadata", make_resultdicts_b, "metadata")
workflow.connect(inputnode, "mask", make_resultdicts_b, "mask")
workflow.connect(make_resultdicts_b, "resultdicts", outputnode, "resultdicts")
#
merge_resultdicts = pe.Node(niu.Merge(2), name="merge_resultdicts")
workflow.connect(make_resultdicts_a, "resultdicts", merge_resultdicts, "in1")
workflow.connect(make_resultdicts_b, "resultdicts", merge_resultdicts, "in2")
resultdict_datasink = pe.Node(
ResultdictDatasink(base_directory=workdir), name="resultdict_datasink"
)
workflow.connect(merge_resultdicts, "out", resultdict_datasink, "indicts")
# parse condition files into three (ordered) lists
parseconditionfile = pe.Node(ParseConditionFile(), name="parseconditionfile")
workflow.connect(inputnode, "condition_names", parseconditionfile, "condition_names")
workflow.connect(inputnode, "condition_files", parseconditionfile, "in_any")
fillna = pe.Node(FillNA(), name="fillna")
workflow.connect(inputnode, "confounds_selected", fillna, "in_tsv")
# first level model specification
modelspec = pe.Node(model.SpecifyModel(), name="modelspec")
if hasattr(feature, "high_pass_filter_cutoff"):
modelspec.inputs.high_pass_filter_cutoff = feature.high_pass_filter_cutoff
else:
modelspec.inputs.high_pass_filter_cutoff = np.inf
workflow.connect(inputnode, "bold", modelspec, "functional_runs")
workflow.connect(inputnode, "condition_units", modelspec, "input_units")
workflow.connect(inputnode, "repetition_time", modelspec, "time_repetition")
workflow.connect(fillna, "out_no_header", modelspec, "realignment_parameters")
workflow.connect(parseconditionfile, "subject_info", modelspec, "subject_info")
# transform contrasts dictionary to nipype list data structure
contrasts = []
if feature is not None:
condition_names = feature.conditions
for contrast in feature.contrasts:
contrast_values = [contrast["values"].get(c, 0.0) for c in condition_names]
contrasts.append(
[contrast["name"], contrast["type"].upper(), condition_names, contrast_values]
)
contrast_names = list(map(firststr, contrasts))
make_resultdicts_b.inputs.taskcontrast = contrast_names
# generate design from first level specification
level1design = pe.Node(
fsl.Level1Design(
contrasts=contrasts,
model_serial_correlations=True,
bases={"dgamma": {"derivs": False}},
),
name="level1design",
)
workflow.connect(inputnode, "repetition_time", level1design, "interscan_interval")
workflow.connect(modelspec, "session_info", level1design, "session_info")
# generate required input files for FILMGLS from design
modelgen = pe.Node(fsl.FEATModel(), name="modelgen")
workflow.connect([(level1design, modelgen, [(("fsf_files", firststr), "fsf_file")])])
workflow.connect([(level1design, modelgen, [(("ev_files", ravel), "ev_files")])])
# calculate range of image values to determine cutoff value
stats = pe.Node(fsl.ImageStats(op_string="-R"), name="stats")
workflow.connect(inputnode, "bold", stats, "in_file")
cutoff = pe.Node(
niu.Function(input_names=["obj"], output_names=["min_val"], function=firstfloat),
name="cutoff",
)
workflow.connect(stats, "out_stat", cutoff, "obj")
# actually estimate the first level model
modelestimate = pe.Node(
fsl.FILMGLS(smooth_autocorr=True, mask_size=5),
name="modelestimate"
)
workflow.connect(inputnode, "bold", modelestimate, "in_file")
workflow.connect(cutoff, "min_val", modelestimate, "threshold")
workflow.connect(modelgen, "design_file", modelestimate, "design_file")
workflow.connect(modelgen, "con_file", modelestimate, "tcon_file")
# make dof volume
makedofvolume = pe.Node(
MakeDofVolume(), iterfield=["dof_file", "copes"], name="makedofvolume"
)
workflow.connect(modelestimate, "copes", makedofvolume, "copes")
workflow.connect(modelestimate, "dof_file", makedofvolume, "dof_file")
workflow.connect(modelestimate, "copes", make_resultdicts_b, "effect")
workflow.connect(modelestimate, "varcopes", make_resultdicts_b, "variance")
workflow.connect(modelestimate, "zstats", make_resultdicts_b, "z")
workflow.connect(makedofvolume, "out_file", make_resultdicts_b, "dof")
#
mergecolumnnames = pe.Node(niu.Merge(2), name="mergecolumnnames")
mergecolumnnames.inputs.in1 = condition_names
workflow.connect(fillna, "column_names", mergecolumnnames, "in2")
design_unvest = pe.Node(Unvest(), name="design_unvest")
workflow.connect(modelgen, "design_file", design_unvest, "in_vest")
design_tsv = pe.Node(MergeColumns(1), name="design_tsv")
workflow.connect(design_unvest, "out_no_header", design_tsv, "in1")
workflow.connect(mergecolumnnames, "out", design_tsv, "column_names1")
contrast_unvest = pe.Node(Unvest(), name="contrast_unvest")
workflow.connect(modelgen, "con_file", contrast_unvest, "in_vest")
contrast_tsv = pe.Node(MergeColumns(1), name="contrast_tsv")
contrast_tsv.inputs.row_index = contrast_names
workflow.connect(contrast_unvest, "out_no_header", contrast_tsv, "in1")
workflow.connect(mergecolumnnames, "out", contrast_tsv, "column_names1")
workflow.connect(design_tsv, "out_with_header", make_resultdicts_a, "design_matrix")
workflow.connect(contrast_tsv, "out_with_header", make_resultdicts_a, "contrast_matrix")
return workflow
def modelfit_fsl(wf_name='modelfit'):
"""
Fit 1st level GLM using FSL routines
Usage (TODO)
modelfit.inputs.inputspec.fwhm = 12
modelfit.inputs.inputspec.brain_mask = ['/opt/shared2/nipype-test/testblock/example_func_brain_mask.nii.gz', '/opt/shared2/nipype-test/testblock/example_func_brain_mask.nii.gz']
modelfit.inputs.inputspec.input_units = 'secs'
modelfit.inputs.inputspec.in_file = ['/opt/shared2/nipype-test/testblock/mc_data_brain.nii.gz', '/opt/shared2/nipype-test/testblock/mc_data_brain.nii.gz']
modelfit.inputs.inputspec.TR = 2
modelfit.inputs.inputspec.high_pass_filter_cutoff = 100 #sigma in TR
modelfit.inputs.inputspec.event_files = ['/opt/shared2/nipype-test/testblock/a']
cont1 = ['whisker', 'T', ['a', 'a'], [1.0, 0.0]]
cont2 = ['-whisker', 'T', ['a', 'a'], [-1.0, 0.0]]
cont3 = ['Task','F', [cont1, cont2]]
contrasts = [cont1]
modelfit.inputs.inputspec.contrasts = contrasts #TODO: change condition names
modelfit.inputs.inputspec.bases_function = {'dgamma': {'derivs': True}}
modelfit.inputs.inputspec.model_serial_correlations = True
#modelfit.write_graph('graph.dot');
modelfit.write_graph('graph.dot', graph2use='colored');
x=modelfit.run()
#x=modelfit.run(plugin='MultiProc', plugin_args={'n_procs': 8})
server.serve_content(modelfit)
"""
modelfit = pe.Workflow(name=wf_name)
"""
Set up a node to define all inputs required for the preprocessing workflow
"""
inputnode = pe.Node(interface=util.IdentityInterface(
fields=[
'in_file', 'ev_file', 'confounders', 'contrasts',
'high_pass_filter_cutoff', 'fwhm', 'interscan_interval', 'TR',
'input_units', 'bases_function', 'model_serial_correlations',
'brain_mask'
],
mandatory_inputs=True),
name='inputspec')
#TODO: eliminate brain mask
#inputnode.iterables=[('high_pass_filter_cutoff', [30, 60, 90, 120, 500])]
"""
Set up a node to define outputs for the preprocessing workflow
"""
outputnode = pe.Node(interface=util.IdentityInterface(
fields=['zstats', 'zfstats', 'copes', 'varcopes'],
mandatory_inputs=True),
name='outputspec')
# collect subject info
getsubjectinfo = pe.MapNode(util.Function(
input_names=['ev_file', 'confounders'],
output_names=['subject_info'],
function=get_subject_info),
name='getsubjectinfo',
iterfield=['confounders'])
# nipype.algorithms.modelgen.SpecifyModel to generate design information.
modelspec = pe.MapNode(interface=model.SpecifyModel(),
name="modelspec",
iterfield=['subject_info'])
# smooth #TODO: move into preproc pipeline
smooth = preproc.create_susan_smooth("smooth")
#smooth.get_node( "smooth").iterables=[('fwhm', [6., 8., 10., 12., 14., 16.])]
toSigma = pe.Node(interface=util.Function(
input_names=['high_pass_filter_cutoff', 'TR'],
output_names=['high_pass_filter_opstring'],
function=highpass_operand),
name='toSigma')
highpass = pe.MapNode(interface=fsl.ImageMaths(suffix='_tempfilt',
op_string=''),
iterfield=['in_file'],
name='highpass')
# Use nipype.interfaces.fsl.Level1Design to generate a run specific fsf file for analysis
level1design = pe.MapNode(interface=fsl.Level1Design(),
name="level1design",
iterfield='session_info')
# Use nipype.interfaces.fsl.FEATModel to generate a run specific mat file for use by FILMGLS
modelgen = pe.MapNode(interface=fsl.FEATModel(),
name='modelgen',
iterfield=['fsf_file', 'ev_files'])
# Use nipype.interfaces.fsl.FILMGLS to estimate a model specified by a mat file and a functional run
modelestimate = pe.MapNode(
interface=fsl.FILMGLS(smooth_autocorr=True, mask_size=5,
threshold=200),
name='modelestimate',
#iterfield=['design_file', 'in_file'])
iterfield=['in_file', 'design_file'])
# Use nipype.interfaces.fsl.ContrastMgr to generate contrast estimates
conestimate = pe.MapNode(interface=fsl.ContrastMgr(),
name='conestimate',
iterfield=[
'param_estimates', 'sigmasquareds',
'corrections', 'dof_file', 'tcon_file'
])
modelfit.connect([
(
inputnode,
smooth,
[
('in_file', 'inputnode.in_files'),
('fwhm', 'inputnode.fwhm'), # in iterable
('brain_mask', 'inputnode.mask_file')
]),
(smooth, highpass, [('outputnode.smoothed_files', 'in_file')]),
(inputnode, toSigma, [('high_pass_filter_cutoff',
'high_pass_filter_cutoff')]),
(inputnode, toSigma, [('TR', 'TR')]),
(toSigma, highpass, [('high_pass_filter_opstring', 'op_string')]),
(inputnode, getsubjectinfo, [('ev_file', 'ev_file'),
('confounders', 'confounders')]),
(getsubjectinfo, modelspec, [('subject_info', 'subject_info')]),
(highpass, modelspec, [('out_file', 'functional_runs')]),
(highpass, modelestimate, [('out_file', 'in_file')]),
(inputnode, modelspec, [
('input_units', 'input_units'),
('TR', 'time_repetition'),
('high_pass_filter_cutoff', 'high_pass_filter_cutoff'),
]),
(inputnode, level1design, [('TR', 'interscan_interval'),
('model_serial_correlations',
'model_serial_correlations'),
('bases_function', 'bases'),
('contrasts', 'contrasts')]),
(modelspec, level1design, [('session_info', 'session_info')]),
(level1design, modelgen, [('fsf_files', 'fsf_file'),
('ev_files', 'ev_files')]),
(modelgen, modelestimate, [('design_file', 'design_file')]),
(modelgen, conestimate, [('con_file', 'tcon_file')]),
(modelestimate, conestimate, [('param_estimates', 'param_estimates'),
('sigmasquareds', 'sigmasquareds'),
('corrections', 'corrections'),
('dof_file', 'dof_file')]),
(conestimate, outputnode, [('zstats', 'zstats'),
('zfstats', 'zfstats'), ('copes', 'copes'),
('varcopes', 'varcopes')])
])
return modelfit
def create_modelfit_workflow(name='modelfit'):
"""Create an FSL individual modelfitting workflow
Example
-------
>>> modelfit = create_modelfit_workflow()
>>> modelfit.base_dir = '.'
>>> info = dict()
>>> modelfit.inputs.inputspec.session_info = info
>>> modelfit.inputs.inputspec.interscan_interval = 3.
>>> modelfit.inputs.inputspec.film_threshold = 1000
>>> modelfit.run() #doctest: +SKIP
Inputs::
inputspec.session_info : info generated by modelgen.SpecifyModel
inputspec.interscan_interval : interscan interval
inputspec.contrasts : list of contrasts
inputspec.film_threshold : image threshold for FILM estimation
Outputs::
outputspec.realignment_parameters : realignment parameter files
outputspec.smoothed_files : smoothed functional files
outputspec.outlier_files : list of outliers
outputspec.outlier_stats : statistics of outliers
outputspec.outlier_plots : images of outliers
outputspec.mask_file : binary mask file in reference image space
outputspec.reg_file : registration file that maps reference image to
freesurfer space
outputspec.reg_cost : cost of registration (useful for detecting
misalignment)
"""
modelfit = pe.Workflow(name=name)
"""
Create the nodes
"""
inputspec = pe.Node(util.IdentityInterface(fields=['session_info',
'interscan_interval',
'contrasts',
'film_threshold',
'functional_data',
'bases',
'model_serial_correlations']),
name='inputspec')
level1design = pe.Node(interface=fsl.Level1Design(), name="level1design")
modelgen = pe.MapNode(interface=fsl.FEATModel(), name='modelgen',
iterfield=['fsf_file', 'ev_files'])
modelestimate = pe.MapNode(interface=fsl.FILMGLS(smooth_autocorr=True,
mask_size=5),
name='modelestimate',
iterfield=['design_file', 'in_file'])
conestimate = pe.MapNode(interface=fsl.ContrastMgr(), name='conestimate',
iterfield=['tcon_file', 'param_estimates',
'sigmasquareds', 'corrections',
'dof_file'])
ztopval = pe.MapNode(interface=fsl.ImageMaths(op_string='-ztop',
suffix='_pval'),
name='ztop',
iterfield=['in_file'])
outputspec = pe.Node(util.IdentityInterface(fields=['copes', 'varcopes',
'dof_file', 'pfiles',
'parameter_estimates']),
name='outputspec')
"""
Utility function
"""
pop_lambda = lambda x: x[0]
"""
Setup the connections
"""
modelfit.connect([
(inputspec, level1design, [('interscan_interval', 'interscan_interval'),
('session_info', 'session_info'),
('contrasts', 'contrasts'),
('bases', 'bases'),
('model_serial_correlations',
'model_serial_correlations')]),
(inputspec, modelestimate, [('film_threshold', 'threshold'),
('functional_data', 'in_file')]),
(level1design, modelgen, [('fsf_files', 'fsf_file'),
('ev_files', 'ev_files')]),
(modelgen, modelestimate, [('design_file', 'design_file')]),
(modelgen, conestimate, [('con_file', 'tcon_file')]),
(modelestimate, conestimate, [('param_estimates', 'param_estimates'),
('sigmasquareds', 'sigmasquareds'),
('corrections', 'corrections'),
('dof_file', 'dof_file')]),
(conestimate, ztopval, [(('zstats', pop_lambda), 'in_file')]),
(ztopval, outputspec, [('out_file', 'pfiles')]),
(modelestimate, outputspec, [('param_estimates', 'parameter_estimates'),
('dof_file', 'dof_file')]),
(conestimate, outputspec, [('copes', 'copes'),
('varcopes', 'varcopes')]),
])
return modelfit
def init_taskbased_wf(analysis=None, memcalc=MemoryCalculator()):
"""
create workflow to calculate a first level glm for task functional data
"""
assert isinstance(analysis, Analysis)
assert isinstance(analysis.tags, Tags)
# make bold file variant specification
boldfilefields = ["bold_file"]
varianttupls = [("space", analysis.tags.space)]
if analysis.tags.grand_mean_scaled is not None:
assert isinstance(analysis.tags.grand_mean_scaled, GrandMeanScaledTag)
varianttupls.append(analysis.tags.grand_mean_scaled.as_tupl())
if analysis.tags.band_pass_filtered is not None:
assert isinstance(analysis.tags.band_pass_filtered,
BandPassFilteredTag)
assert analysis.tags.band_pass_filtered.type == "gaussian"
varianttupls.append(analysis.tags.band_pass_filtered.as_tupl())
if analysis.tags.confounds_removed is not None:
assert isinstance(analysis.tags.confounds_removed, ConfoundsRemovedTag)
confounds_removed_names = tuple(
name for name in analysis.tags.confounds_removed.names
if "aroma_motion" in name)
varianttupls.append(("confounds_removed", confounds_removed_names))
confounds_extract_names = tuple(
name for name in analysis.tags.confounds_removed.names
if "aroma_motion" not in name)
if len(confounds_extract_names) > 0:
boldfilefields.append("confounds_file")
varianttupls.append(("confounds_extract", confounds_extract_names))
if analysis.tags.smoothed is not None:
assert isinstance(analysis.tags.smoothed, SmoothedTag)
varianttupls.append(analysis.tags.smoothed.as_tupl())
variantdict = dict(varianttupls)
boldfilevariant = (tuple(boldfilefields), tuple(varianttupls))
assert analysis.name is not None
workflow = pe.Workflow(name=analysis.name)
# inputs are the bold file, the mask file and the confounds file
inputnode = pe.Node(
niu.IdentityInterface(fields=[
*boldfilefields, "mask_file", "condition_files", "metadata"
]),
name="inputnode",
)
# parse condition files into three (ordered) lists
parseconditionfile = pe.Node(
interface=ParseConditionFile(),
name="parseconditionfile",
)
workflow.connect(inputnode, "condition_files", parseconditionfile,
"in_any")
def get_repetition_time(dic):
return dic.get("RepetitionTime")
# first level model specification
modelspec = pe.Node(
interface=model.SpecifyModel(input_units="secs", ),
name="modelspec",
)
workflow.connect([
(
inputnode,
modelspec,
[
("bold_file", "functional_runs"),
(("metadata", get_repetition_time), "time_repetition"),
],
),
(parseconditionfile, modelspec, [("subject_info", "subject_info")]),
])
if "band_pass_filtered" in variantdict:
modelspec.inputs.high_pass_filter_cutoff = float(
analysis.tags.band_pass_filtered.high)
if "confounds_extract" in variantdict:
workflow.connect([(inputnode, modelspec,
[("confounds_file", "realignment_parameters")])])
# transform contrasts dictionary to nipype list data structure
contrasts = [[
contrast.name,
contrast.type.upper(), *map(list, zip(*contrast.values.items()))
] for contrast in analysis.contrasts]
# generate design from first level specification
level1design = pe.Node(
interface=fsl.Level1Design(
contrasts=contrasts,
model_serial_correlations=True,
bases={"dgamma": {
"derivs": False
}},
),
name="level1design",
)
workflow.connect([
(
inputnode,
level1design,
[(("metadata", get_repetition_time), "interscan_interval")],
),
(modelspec, level1design, [("session_info", "session_info")]),
])
# generate required input files for FILMGLS from design
modelgen = pe.Node(interface=fsl.FEATModel(),
name="modelgen",
iterfield=["fsf_file", "ev_files"])
workflow.connect([(
level1design,
modelgen,
[("fsf_files", "fsf_file"), ("ev_files", "ev_files")],
)])
# calculate range of image values to determine cutoff value
# for FILMGLS
boldfilecutoff = pe.Node(interface=fsl.ImageStats(op_string="-R"),
name="boldfilecutoff")
workflow.connect([(inputnode, boldfilecutoff, [("bold_file", "in_file")])])
# actually estimate the first level model
modelestimate = pe.Node(
interface=fsl.FILMGLS(smooth_autocorr=True, mask_size=5),
name="modelestimate",
iterfield=["design_file", "in_file", "tcon_file"],
)
workflow.connect([
(inputnode, modelestimate, [("bold_file", "in_file")]),
(boldfilecutoff, modelestimate, [(("out_stat", firstfloat),
"threshold")]),
(
modelgen,
modelestimate,
[("design_file", "design_file"), ("con_file", "tcon_file")],
),
])
# make dof volume
makedofvolume = pe.MapNode(
interface=MakeDofVolume(),
iterfield=["dof_file", "cope_file"],
name="makedofvolume",
)
workflow.connect([
(
modelestimate,
makedofvolume,
[(("copes", first), "cope_file"), ("dof_file", "dof_file")],
),
])
outputnode = pe.Node(
interface=MakeResultdicts(keys=[
"firstlevelanalysisname",
"firstlevelfeaturename",
"cope",
"varcope",
"zstat",
"dof_file",
"mask_file",
]),
name="outputnode",
)
outputnode.inputs.firstlevelanalysisname = analysis.name
outputnode.inputs.firstlevelfeaturename = list(map(first, contrasts))
workflow.connect([
(inputnode, outputnode, [("metadata", "basedict"),
("mask_file", "mask_file")]),
(
modelestimate,
outputnode,
[
(("copes", ravel), "cope"),
(("varcopes", ravel), "varcope"),
(("zstats", ravel), "zstat"),
],
),
(makedofvolume, outputnode, [("out_file", "dof_file")]),
])
return workflow, (boldfilevariant, )
###########
#
# SETTING UP THE FIRST LEVEL ANALYSIS NODES
#
###########
# model specification
modelspec = Node(modelgen.SpecifyModel(subject_info=subject_info,
input_units='secs',
time_repetition=TR,
high_pass_filter_cutoff=100),
name="modelspec")
# first-level design
level1design = Node(fsl.Level1Design(bases={'dgamma':{'derivs': True}},
interscan_interval=TR,
model_serial_correlations=True,
contrasts=contrast_list),
name="level1design")
# creating all the other files necessary to run the model
modelgen = Node(fsl.FEATModel(),
name='modelgen')
# then running through FEAT
feat = Node(fsl.FEAT(),
name="feat")
# creating datasink to collect outputs
datasink = Node(DataSink(base_directory=outDir),
name='datasink')
def create_first(name='modelfit'):
"""First level task-fMRI modelling workflow
Parameters
----------
name : name of workflow. Default = 'modelfit'
Inputs
------
inputspec.session_info :
inputspec.interscan_interval :
inputspec.contrasts :
inputspec.film_threshold :
inputspec.functional_data :
inputspec.bases :
inputspec.model_serial_correlations :
Outputs
-------
outputspec.copes :
outputspec.varcopes :
outputspec.dof_file :
outputspec.pfiles :
outputspec.parameter_estimates :
outputspec.zstats :
outputspec.tstats :
outputspec.design_image :
outputspec.design_file :
outputspec.design_cov :
Returns
-------
workflow : first-level workflow
"""
import nipype.interfaces.fsl as fsl # fsl
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as util
modelfit = pe.Workflow(name=name)
inputspec = pe.Node(util.IdentityInterface(fields=[
'session_info', 'interscan_interval', 'contrasts', 'film_threshold',
'functional_data', 'bases', 'model_serial_correlations'
]),
name='inputspec')
level1design = pe.Node(interface=fsl.Level1Design(),
name="create_level1_design")
modelgen = pe.MapNode(interface=fsl.FEATModel(),
name='generate_model',
iterfield=['fsf_file', 'ev_files'])
modelestimate = pe.MapNode(interface=fsl.FILMGLS(smooth_autocorr=True,
mask_size=5),
name='estimate_model',
iterfield=['design_file', 'in_file'])
conestimate = pe.MapNode(interface=fsl.ContrastMgr(),
name='estimate_contrast',
iterfield=[
'tcon_file', 'param_estimates',
'sigmasquareds', 'corrections', 'dof_file'
])
ztopval = pe.MapNode(interface=fsl.ImageMaths(op_string='-ztop',
suffix='_pval'),
name='z2pval',
iterfield=['in_file'])
outputspec = pe.Node(util.IdentityInterface(fields=[
'copes', 'varcopes', 'dof_file', 'pfiles', 'parameter_estimates',
'zstats', 'tstats', 'design_image', 'design_file', 'design_cov',
'sigmasquareds'
]),
name='outputspec')
# Utility function
pop_lambda = lambda x: x[0]
# Setup the connections
modelfit.connect([
(inputspec, level1design,
[('interscan_interval', 'interscan_interval'),
('session_info', 'session_info'), ('contrasts', 'contrasts'),
('bases', 'bases'),
('model_serial_correlations', 'model_serial_correlations')]),
(inputspec, modelestimate, [('film_threshold', 'threshold'),
('functional_data', 'in_file')]),
(level1design, modelgen, [('fsf_files', 'fsf_file'),
('ev_files', 'ev_files')]),
(modelgen, modelestimate, [('design_file', 'design_file')]),
(modelgen, conestimate, [('con_file', 'tcon_file')]),
(modelestimate, conestimate, [('param_estimates', 'param_estimates'),
('sigmasquareds', 'sigmasquareds'),
('corrections', 'corrections'),
('dof_file', 'dof_file')]),
(conestimate, ztopval, [(('zstats', pop_lambda), 'in_file')]),
(ztopval, outputspec, [('out_file', 'pfiles')]),
(modelestimate, outputspec, [('param_estimates',
'parameter_estimates'),
('dof_file', 'dof_file'),
('sigmasquareds', 'sigmasquareds')]),
(conestimate, outputspec, [('copes', 'copes'),
('varcopes', 'varcopes'),
('tstats', 'tstats'), ('zstats', 'zstats')])
])
modelfit.connect(modelgen, 'design_image', outputspec, 'design_image')
modelfit.connect(modelgen, 'design_file', outputspec, 'design_file')
modelfit.connect(modelgen, 'design_cov', outputspec, 'design_cov')
return modelfit
contrasts = [cont1, cont2, cont3, cont4, cont5]
#%%
l1_spec = pe.Node(SpecifyModel(
parameter_source='FSL',
input_units='secs',
high_pass_filter_cutoff=120,
time_repetition = tr,
), name='l1_spec')
# l1_model creates a first-level model design
l1_model = pe.Node(fsl.Level1Design(
bases={'dgamma': {'derivs': True}},
model_serial_correlations=True,
interscan_interval = tr,
contrasts=contrasts
# orthogonalization=orthogonality,
), name='l1_model')
# feat_spec generates an fsf model specification file
feat_spec = pe.Node(fsl.FEATModel(), name='feat_spec')
# feat_fit actually runs FEAT
feat_fit = pe.Node(fsl.FEAT(), name='feat_fit', mem_gb=5)
## instead of FEAT
#modelestimate = pe.MapNode(interface=fsl.FILMGLS(smooth_autocorr=True,
# mask_size=5,
# threshold=1000),
# name='modelestimate',
name="Target_ModelSpec",
iterfield=[
'event_files', 'functional_runs', 'realignment_parameters'
])
analysis.connect(data, 'ev_target', target_modelspec,
'event_files')
analysis.connect(question_trimmer, ('roi_file', nest_list),
target_modelspec, 'functional_runs')
analysis.connect(mp_trimmer, ('trimmed', nest_list),
target_modelspec, 'realignment_parameters')
target_level1design = MapNode(
interface=fsl.Level1Design(bases={'dgamma': {
'derivs': False
}},
interscan_interval=.400,
model_serial_correlations=True),
name="Target_level1design",
iterfield=['session_info', 'contrasts'])
analysis.connect(target_modelspec, 'session_info',
target_level1design, 'session_info')
analysis.connect(data, 'target_contrasts', target_level1design,
'contrasts')
target_FEATModel = MapNode(interface=fsl.model.FEATModel(),
name='Target_FEATModel',
iterfield=['ev_files', 'fsf_file'])
analysis.connect(target_level1design, ('ev_files', unnest_list),
target_FEATModel, 'ev_files')
analysis.connect(target_level1design, ('fsf_files', unnest_list),
def L1PIPE():
# ---1) Import modules
import nipype.interfaces.fsl as fsl
import nipype.pipeline.engine as pe
import nipype.algorithms.modelgen as model
import glob
from nipype import Function
import matplotlib
import nipype.interfaces.utility as util
import os
#--- 2) Specify model node
specify_model = pe.Node(interface=model.SpecifyModel(), name="SPECIFY_MODEL")
specify_model.inputs.input_units = 'secs'
runs=raw_input('Please drag in the pre-processsed functional data\n')
runs2= runs.strip('\'"')
NIFTIDIR=os.path.split(runs2)[0]
specify_model.inputs.functional_runs = [runs2]
specify_model.inputs.time_repetition = float(raw_input('Enter the TR (s)\n'))
specify_model.inputs.high_pass_filter_cutoff = float(raw_input('Enter the High pass filter cutoff (s)\n'))
EVENTFILES=raw_input('Please drag in the directory of 3 column event files')
EVENTFILES2=EVENTFILES.strip('\'"')
EVENTFILESLIST=glob.glob(EVENTFILES2 + '/*')
specify_model.inputs.event_files=sorted(EVENTFILESLIST)
#--- 3) Level 1 design node.
Designer=pe.Node(interface=fsl.Level1Design(),name='DESIGN')
Designer.inputs.interscan_interval = float(specify_model.inputs.time_repetition)
Designer.inputs.bases = {'dgamma':{'derivs': False}}
Designer.inputs.model_serial_correlations=bool(0)
#--- 4) Make some contrasts
cont1=('Task', 'T', ['B1INVFEAR.RUN001', 'B1INVINVFEAR.RUN001', 'B1INVINVNEUT.RUN001', 'B1INVNEUT.RUN001', 'B1SCFEAR.RUN001', 'B1SCNEUT.RUN001', 'B1UPFEAR.RUN001', 'B1UPINVFEAR.RUN001', 'B1UPINVNEUT.RUN001', 'B1UPNEUT.RUN001'], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1])
cont2=('Up', 'T', ['B1INVFEAR.RUN001', 'B1INVINVFEAR.RUN001', 'B1INVINVNEUT.RUN001', 'B1INVNEUT.RUN001', 'B1SCFEAR.RUN001', 'B1SCNEUT.RUN001', 'B1UPFEAR.RUN001', 'B1UPINVFEAR.RUN001', 'B1UPINVNEUT.RUN001', 'B1UPNEUT.RUN001'], [0, 0, 0, 0, 0, 0, 1, 0, 0, 1])
cont3=('SC', 'T', ['B1INVFEAR.RUN001', 'B1INVINVFEAR.RUN001', 'B1INVINVNEUT.RUN001', 'B1INVNEUT.RUN001', 'B1SCFEAR.RUN001', 'B1SCNEUT.RUN001', 'B1UPFEAR.RUN001', 'B1UPINVFEAR.RUN001', 'B1UPINVNEUT.RUN001', 'B1UPNEUT.RUN001'], [0, 0, 0, 0, 1, 1, 0, 0, 0, 0])
cont4=('UpvSC', 'T', ['B1INVFEAR.RUN001', 'B1INVINVFEAR.RUN001', 'B1INVINVNEUT.RUN001', 'B1INVNEUT.RUN001', 'B1SCFEAR.RUN001', 'B1SCNEUT.RUN001', 'B1UPFEAR.RUN001', 'B1UPINVFEAR.RUN001', 'B1UPINVNEUT.RUN001', 'B1UPNEUT.RUN001'], [0, 0, 0, 0, -1, -1, 1, 0, 0, 1])
Designer.inputs.contrasts=[cont1, cont2, cont3, cont4]
#--- 5) FSL model node
Model=pe.Node(interface=fsl.FEATModel(),name='FEATMODEL')
#--- 6) FILM GSL node
fgls=pe.Node(interface=fsl.FILMGLS(),name='FILM_GLS')
fgls.inputs.in_file=runs2
#--- 7) outputnode for the design image (gets binned otherwise)
outputnode = pe.Node(interface=util.IdentityInterface(fields=['im','cope','varcope','dof','resid','params','sigmas']),name='outputnode')
#--- 8) Plotting node
def plot(in_file):
from nilearn import image
from nilearn import plotting
import matplotlib
display=plotting.plot_stat_map(stat_map_img = in_file, display_mode='z', cut_coords=10, threshold=float(0))
matplotlib.pyplot.show()
plotter=pe.MapNode(Function(input_names=['in_file'],output_names='display',function=plot),iterfield=['in_file'],name='PLOTTER')
workflow = pe.Workflow(name='L1PIPE')
workflow.connect(specify_model,'session_info',Designer,'session_info')
workflow.connect(Designer,'fsf_files',Model,'fsf_file')
workflow.connect(Designer,'ev_files',Model,'ev_files')
workflow.connect(Model,'design_file',fgls,'design_file')
workflow.connect(Model,'con_file',fgls,'tcon_file')
workflow.connect(Model,'design_image',outputnode,'im')
# Feed the z stats to the plotter.
workflow.connect(fgls,'zstats',plotter,'in_file')
workflow.connect(fgls,'copes',outputnode,'cope')
workflow.connect(fgls,'varcopes',outputnode,'varcope')
workflow.connect(fgls,'dof_file',outputnode,'dof')
workflow.connect(fgls,'residual4d',outputnode,'resid')
workflow.connect(fgls,'param_estimates',outputnode,'params')
workflow.connect(fgls,'sigmasquareds',outputnode,'sigmas')
workflow.base_dir = NIFTIDIR
workflow.write_graph(graph2use='exec')
workflow.run()
def init_glm_wf(conditions,
contrasts,
repetition_time,
use_mov_pars,
name="glm"):
"""
create workflow to calculate a first level glm for task functional data
:param conditions: dictionary of conditions with onsets and durations
by condition names
:param contrasts: dictionary of contrasts by names
:param repetition_time: repetition time
:param use_mov_pars: if true, regress out movement parameters when
calculating the glm
:param name: workflow name (Default value = "glm")
"""
workflow = pe.Workflow(name=name)
# inputs are the bold file, the mask file and the confounds file
# that contains the movement parameters
inputnode = pe.Node(niu.IdentityInterface(
fields=["bold_file", "mask_file", "confounds_file"]),
name="inputnode")
# transform (unordered) conditions dictionary into three (ordered) lists
names = list(conditions.keys())
onsets = [conditions[k]["onsets"] for k in names]
durations = [conditions[k]["durations"] for k in names]
# first level model specification
modelspec = pe.Node(interface=model.SpecifyModel(
input_units="secs",
high_pass_filter_cutoff=128.,
time_repetition=repetition_time,
subject_info=Bunch(conditions=names,
onsets=onsets,
durations=durations)),
name="modelspec")
# transform contrasts dictionary to nipype list data structure
contrasts_ = [[k, "T"] +
[list(i) for i in zip(*[(n, val) for n, val in v.items()])]
for k, v in contrasts.items()]
connames = [k[0] for k in contrasts_]
# outputs are cope, varcope and zstat for each contrast and a dof_file
outputnode = pe.Node(niu.IdentityInterface(fields=sum(
[["%s_img" % conname,
"%s_varcope" % conname,
"%s_zstat" % conname] for conname in connames], []) + ["dof_file"]),
name="outputnode")
outputnode._interface.names = connames
# generate design from first level specification
level1design = pe.Node(interface=fsl.Level1Design(
contrasts=contrasts_,
interscan_interval=repetition_time,
model_serial_correlations=True,
bases={"dgamma": {
"derivs": False
}}),
name="level1design")
# generate required input files for FILMGLS from design
modelgen = pe.Node(interface=fsl.FEATModel(),
name="modelgen",
iterfield=["fsf_file", "ev_files"])
# calculate range of image values to determine cutoff value
# for FILMGLS
stats = pe.Node(interface=fsl.ImageStats(op_string="-R"), name="stats")
# actuallt estimate the firsy level model
modelestimate = pe.Node(interface=fsl.FILMGLS(smooth_autocorr=True,
mask_size=5),
name="modelestimate",
iterfield=["design_file", "in_file", "tcon_file"])
# mask regression outputs
maskimgs = pe.MapNode(interface=fsl.ApplyMask(),
name="maskimgs",
iterfield=["in_file"])
maskvarcopes = pe.MapNode(interface=fsl.ApplyMask(),
name="maskvarcopes",
iterfield=["in_file"])
maskzstats = pe.MapNode(interface=fsl.ApplyMask(),
name="maskzstats",
iterfield=["in_file"])
# split regression outputs by name
splitimgs = pe.Node(interface=niu.Split(splits=[1
for conname in connames]),
name="splitimgs")
splitvarcopes = pe.Node(
interface=niu.Split(splits=[1 for conname in connames]),
name="splitvarcopes")
splitzstats = pe.Node(
interface=niu.Split(splits=[1 for conname in connames]),
name="splitzstats")
# pass movement parameters to glm model specification if requested
c = [("bold_file", "functional_runs")]
if use_mov_pars:
c.append(("confounds_file", "realignment_parameters"))
workflow.connect([
(inputnode, modelspec, c),
(inputnode, modelestimate, [("bold_file", "in_file")]),
(modelspec, level1design, [("session_info", "session_info")]),
(level1design, modelgen, [("fsf_files", "fsf_file"),
("ev_files", "ev_files")]),
(inputnode, stats, [("bold_file", "in_file")]),
(stats, modelestimate, [(("out_stat", get_float), "threshold")]),
(modelgen, modelestimate, [("design_file", "design_file"),
("con_file", "tcon_file")]),
(inputnode, maskimgs, [("mask_file", "mask_file")]),
(inputnode, maskvarcopes, [("mask_file", "mask_file")]),
(inputnode, maskzstats, [("mask_file", "mask_file")]),
(modelestimate, maskimgs, [
(("copes", flatten), "in_file"),
]),
(modelestimate, maskvarcopes, [
(("varcopes", flatten), "in_file"),
]),
(modelestimate, maskzstats, [
(("zstats", flatten), "in_file"),
]),
(modelestimate, outputnode, [("dof_file", "dof_file")]),
(maskimgs, splitimgs, [
("out_file", "inlist"),
]),
(maskvarcopes, splitvarcopes, [
("out_file", "inlist"),
]),
(maskzstats, splitzstats, [
("out_file", "inlist"),
]),
])
# connect outputs named for the contrasts
for i, conname in enumerate(connames):
workflow.connect(splitimgs, "out%i" % (i + 1), outputnode,
"%s_img" % conname)
workflow.connect(splitvarcopes, "out%i" % (i + 1), outputnode,
"%s_varcope" % conname)
workflow.connect(splitzstats, "out%i" % (i + 1), outputnode,
"%s_zstat" % conname)
return workflow, connames
#Wraps command **fslmaths**
NodeHash_17446a20 = pe.MapNode(interface = fsl.MeanImage(), name = 'NodeName_17446a20', iterfield = ['in_file'])
NodeHash_17446a20.inputs.dimension = 'T'
#Wraps command **fslmaths**
NodeHash_b5a5810 = pe.MapNode(interface = fsl.BinaryMaths(), name = 'NodeName_b5a5810', iterfield = ['in_file', 'operand_file'])
NodeHash_b5a5810.inputs.operation = 'add'
#Makes a model specification compatible with spm/fsl designers.
NodeHash_1e7a3420 = pe.MapNode(interface = modelgen.SpecifyModel(), name = 'NodeName_1e7a3420', iterfield = ['functional_runs', 'subject_info'])
NodeHash_1e7a3420.inputs.high_pass_filter_cutoff = 0
NodeHash_1e7a3420.inputs.input_units = 'secs'
NodeHash_1e7a3420.inputs.time_repetition = 2.0
#Generate FEAT specific files
NodeHash_9bb0d40 = pe.MapNode(interface = fsl.Level1Design(), name = 'NodeName_9bb0d40', iterfield = ['session_info'])
NodeHash_9bb0d40.inputs.bases = {'dgamma':{'derivs': False}}
NodeHash_9bb0d40.inputs.contrasts = [('con-incon', 'T', ['congruent_correct', 'congruent_correct'], [-1, 1])]
NodeHash_9bb0d40.inputs.interscan_interval = 2.0
NodeHash_9bb0d40.inputs.model_serial_correlations = True
#Wraps command **feat_model**
NodeHash_6b33f50 = pe.MapNode(interface = fsl.FEATModel(), name = 'NodeName_6b33f50', iterfield = ['ev_files', 'fsf_file'])
#Wraps command **film_gls**
NodeHash_2762fb60 = pe.MapNode(interface = fsl.FILMGLS(), name = 'NodeName_2762fb60', iterfield = ['design_file', 'in_file', 'tcon_file'])
#Wraps command **fslmaths**
NodeHash_2df82970 = pe.MapNode(interface = fsl.MeanImage(), name = 'NodeName_2df82970', iterfield = ['in_file'])
NodeHash_2df82970.inputs.dimension = 'T'
datasink.inputs.container = 'results/'
# Model Specs
#Use nipype.algorithms.modelgen.SpecifyModel to generate design information.
modelspec = pe.Node(interface=SpecifyModel(), name="modelspec")
modelspec.inputs.input_units = 'secs'
modelspec.inputs.time_repetition = TR
modelspec.inputs.high_pass_filter_cutoff = high_pass
#Use nipype.interfaces.fsl.Level1Design to generate a run specific fsf file for analysis
level1design = pe.Node(
interface=fsl.Level1Design(
interscan_interval=TR,
model_serial_correlations=modelSerialCorrelations,
bases={'dgamma': {
'derivs': False
}},
contrasts=conts),
name="level1design",
)
#Use nipype.interfaces.fsl.FEATModel to generate a run specific mat file for use by FILMGLS
modelgen = pe.MapNode(
interface=fsl.FEATModel(),
name='modelgen',
iterfield=['fsf_file', 'ev_files'],
)
#Use nipype.interfaces.fsl.FILMGLS to estimate a model specified by a mat file and a functional run
modelestimate = pe.MapNode(interface=fsl.FILMGLS(smooth_autocorr=True,
#Wraps command **fslmaths**
NodeHash_1fdac460 = pe.MapNode(interface=fsl.BinaryMaths(),
name='NodeName_1fdac460',
iterfield=['in_file', 'operand_file'])
NodeHash_1fdac460.inputs.operation = 'add'
#Makes a model specification compatible with spm/fsl designers.
NodeHash_214dcae0 = pe.MapNode(interface=modelgen.SpecifyModel(),
name='NodeName_214dcae0',
iterfield=['functional_runs', 'subject_info'])
NodeHash_214dcae0.inputs.high_pass_filter_cutoff = 0
NodeHash_214dcae0.inputs.input_units = 'secs'
NodeHash_214dcae0.inputs.time_repetition = 2.0
#Generate FEAT specific files
NodeHash_2087a210 = pe.MapNode(interface=fsl.Level1Design(),
name='NodeName_2087a210',
iterfield=['session_info'])
NodeHash_2087a210.inputs.bases = {'dgamma': {'derivs': False}}
NodeHash_2087a210.inputs.contrasts = [
('con-incon', 'T', ['congruent_correct', 'congruent_correct'], [-1, 1])
]
NodeHash_2087a210.inputs.interscan_interval = 2.0
NodeHash_2087a210.inputs.model_serial_correlations = True
#Wraps command **feat_model**
NodeHash_219c0190 = pe.MapNode(interface=fsl.FEATModel(),
name='NodeName_219c0190',
iterfield=['ev_files', 'fsf_file'])
#Wraps command **film_gls**
def first_level_wf(pipeline, subject_id, task_id, output_dir):
"""
First level workflow
"""
workflow = pe.Workflow(name='_'.join((pipeline, subject_id, task_id)))
inputnode = pe.Node(niu.IdentityInterface(fields=[
'bold_preproc', 'contrasts', 'confounds', 'brainmask', 'events_file'
]),
name='inputnode')
outputnode = pe.Node(
niu.IdentityInterface(fields=['sigma_pre', 'sigma_post', 'out_stats']),
name='outputnode')
conf2movpar = pe.Node(niu.Function(function=_confounds2movpar),
name='conf2movpar')
masker = pe.Node(fsl.ApplyMask(), name='masker')
bim = pe.Node(afni.BlurInMask(fwhm=5.0, outputtype='NIFTI_GZ'),
name='bim',
mem_gb=20)
ev = pe.Node(EventsFilesForTask(task=task_id), name='events')
l1 = pe.Node(SpecifyModel(
input_units='secs',
time_repetition=2,
high_pass_filter_cutoff=100,
parameter_source='FSL',
),
name='l1')
l1model = pe.Node(fsl.Level1Design(interscan_interval=2,
bases={'dgamma': {
'derivs': True
}},
model_serial_correlations=True),
name='l1design')
l1featmodel = pe.Node(fsl.FEATModel(), name='l1model')
l1estimate = pe.Node(fsl.FEAT(), name='l1estimate', mem_gb=40)
pre_smooth_afni = pe.Node(afni.FWHMx(combine=True,
detrend=True,
args='-ShowMeClassicFWHM'),
name='smooth_pre_afni',
mem_gb=20)
post_smooth_afni = pe.Node(afni.FWHMx(combine=True,
detrend=True,
args='-ShowMeClassicFWHM'),
name='smooth_post_afni',
mem_gb=20)
pre_smooth = pe.Node(fsl.SmoothEstimate(), name='smooth_pre', mem_gb=20)
post_smooth = pe.Node(fsl.SmoothEstimate(), name='smooth_post', mem_gb=20)
def _resels(val):
return val**(1 / 3.)
def _fwhm(fwhm):
from numpy import mean
return float(mean(fwhm, dtype=float))
workflow.connect([
(inputnode, masker, [('bold_preproc', 'in_file'),
('brainmask', 'mask_file')]),
(inputnode, ev, [('events_file', 'in_file')]),
(inputnode, l1model, [('contrasts', 'contrasts')]),
(inputnode, conf2movpar, [('confounds', 'in_confounds')]),
(inputnode, bim, [('brainmask', 'mask')]),
(masker, bim, [('out_file', 'in_file')]),
(bim, l1, [('out_file', 'functional_runs')]),
(ev, l1, [('event_files', 'event_files')]),
(conf2movpar, l1, [('out', 'realignment_parameters')]),
(l1, l1model, [('session_info', 'session_info')]),
(ev, l1model, [('orthogonalization', 'orthogonalization')]),
(l1model, l1featmodel, [('fsf_files', 'fsf_file'),
('ev_files', 'ev_files')]),
(l1model, l1estimate, [('fsf_files', 'fsf_file')]),
# Smooth
(inputnode, pre_smooth, [('bold_preproc', 'zstat_file'),
('brainmask', 'mask_file')]),
(bim, post_smooth, [('out_file', 'zstat_file')]),
(inputnode, post_smooth, [('brainmask', 'mask_file')]),
(pre_smooth, outputnode, [(('resels', _resels), 'sigma_pre')]),
(post_smooth, outputnode, [(('resels', _resels), 'sigma_post')]),
# Smooth with AFNI
(inputnode, pre_smooth_afni, [('bold_preproc', 'in_file'),
('brainmask', 'mask')]),
(bim, post_smooth_afni, [('out_file', 'in_file')]),
(inputnode, post_smooth_afni, [('brainmask', 'mask')]),
])
# Writing outputs
csv = pe.Node(AddCSVRow(in_file=str(output_dir / 'smoothness.csv')),
name='addcsv_%s_%s' % (subject_id, pipeline))
csv.inputs.sub_id = subject_id
csv.inputs.pipeline = pipeline
# Datasinks
ds_stats = pe.Node(niu.Function(function=_feat_stats), name='ds_stats')
ds_stats.inputs.subject_id = subject_id
ds_stats.inputs.task_id = task_id
ds_stats.inputs.variant = pipeline
ds_stats.inputs.out_path = output_dir
setattr(ds_stats.interface, '_always_run', True)
workflow.connect([
(outputnode, csv, [('sigma_pre', 'smooth_pre'),
('sigma_post', 'smooth_post')]),
(pre_smooth_afni, csv, [(('fwhm', _fwhm), 'fwhm_pre')]),
(post_smooth_afni, csv, [(('fwhm', _fwhm), 'fwhm_post')]),
(l1estimate, ds_stats, [('feat_dir', 'feat_dir')]),
(ds_stats, outputnode, [('out', 'out_stats')]),
])
return workflow
"""
#Master Node
modelfit = pe.Workflow(name='modelfit')
#generate design information
modelspec = pe.Node(interface=model.SpecifyModel(
input_units=input_units,
time_repetition=TR,
high_pass_filter_cutoff=hpcutoff),
name="modelspec")
#generate a run specific fsf file for analysis
level1design = pe.Node(interface=fsl.Level1Design(
interscan_interval=TR,
bases={'dgamma': {
'derivs': False
}},
contrasts=contrasts,
model_serial_correlations=True),
name="level1design")
#generate a run specific mat file for use by FILMGLS
modelgen = pe.MapNode(interface=fsl.FEATModel(),
name='modelgen',
iterfield=['fsf_file', 'ev_files'])
#estomate Model
modelestimate = pe.MapNode(interface=fsl.FILMGLS(smooth_autocorr=True,
mask_size=5,
threshold=1000),
name='modelestimate',
def fsl_run_level_wf(
model,
step,
bids_dir,
output_dir,
work_dir,
subject_id,
database_path,
smoothing_fwhm=None,
smoothing_level=None,
smoothing_type=None,
use_rapidart=False,
detrend_poly=None,
align_volumes=None,
smooth_autocorrelations=False,
despike=False,
name="fsl_run_level_wf",
):
"""Generate run level workflow for a given model."""
bids_dir = Path(bids_dir)
work_dir = Path(work_dir)
workflow = pe.Workflow(name=name)
level = step["Level"]
dimensionality = 3 # Nipype FSL.SUSAN Default
if smoothing_type == "inp":
dimensionality = 2
workflow.__desc__ = ""
(work_dir / model["Name"]).mkdir(exist_ok=True)
include_entities = {}
if "Input" in model:
if "Include" in model["Input"]:
include_entities = model["Input"]["Include"]
include_entities.update({"subject": subject_id})
getter = pe.Node(
BIDSGet(
database_path=database_path,
fixed_entities=include_entities,
align_volumes=align_volumes,
),
name="func_select",
)
get_info = pe.MapNode(
GetRunModelInfo(model=step, detrend_poly=detrend_poly),
iterfield=[
"metadata_file", "regressor_file", "events_file", "entities"
],
name=f"get_{level}_info",
)
despiker = pe.MapNode(
afni.Despike(outputtype="NIFTI_GZ"),
iterfield=["in_file"],
name="despiker",
)
realign_runs = pe.MapNode(
fsl.MCFLIRT(output_type="NIFTI_GZ", interpolation="sinc"),
iterfield=["in_file", "ref_file"],
name="func_realign",
)
wrangle_volumes = pe.MapNode(
IdentityInterface(fields=["functional_file"]),
iterfield=["functional_file"],
name="wrangle_volumes",
)
specify_model = pe.MapNode(
modelgen.SpecifyModel(high_pass_filter_cutoff=-1.0,
input_units="secs"),
iterfield=["functional_runs", "subject_info", "time_repetition"],
name=f"model_{level}_specify",
)
fit_model = pe.MapNode(
IdentityInterface(
fields=[
"session_info", "interscan_interval", "contrasts",
"functional_data"
],
mandatory_inputs=True,
),
iterfield=[
"functional_data", "session_info", "interscan_interval",
"contrasts"
],
name=f"model_{level}_fit",
)
first_level_design = pe.MapNode(
fsl.Level1Design(
bases={"dgamma": {
"derivs": False
}},
model_serial_correlations=False,
),
iterfield=["session_info", "interscan_interval", "contrasts"],
name=f"model_{level}_design",
)
generate_model = pe.MapNode(
fsl.FEATModel(output_type="NIFTI_GZ"),
iterfield=["fsf_file", "ev_files"],
name=f"model_{level}_generate",
)
estimate_model = pe.MapNode(
fsl.FILMGLS(
threshold=0.0, # smooth_autocorr=True
output_type="NIFTI_GZ",
results_dir="results",
smooth_autocorr=False,
autocorr_noestimate=True,
),
iterfield=["design_file", "in_file", "tcon_file"],
name=f"model_{level}_estimate",
)
if smooth_autocorrelations:
first_level_design.inputs.model_serial_correlations = True
estimate_model.inputs.smooth_autocorr = True
estimate_model.inputs.autocorr_noestimate = False
calculate_p = pe.MapNode(
fsl.ImageMaths(output_type="NIFTI_GZ",
op_string="-ztop",
suffix="_pval"),
iterfield=["in_file"],
name=f"model_{level}_caculate_p",
)
image_pattern = ("[sub-{subject}/][ses-{session}/]"
"[sub-{subject}_][ses-{session}_]"
"task-{task}_[acq-{acquisition}_]"
"[rec-{reconstruction}_][run-{run}_]"
"[echo-{echo}_][space-{space}_]contrast-{contrast}_"
"stat-{stat<effect|variance|z|p|t|F>}_statmap.nii.gz")
run_rapidart = pe.MapNode(
ra.ArtifactDetect(
use_differences=[True, False],
use_norm=True,
zintensity_threshold=3,
norm_threshold=1,
bound_by_brainmask=True,
mask_type="file",
parameter_source="FSL",
),
iterfield=["realignment_parameters", "realigned_files", "mask_file"],
name="rapidart_run",
)
reshape_rapidart = pe.MapNode(
Function(
input_names=[
"run_info", "functional_file", "outlier_file",
"contrast_entities"
],
output_names=["run_info", "contrast_entities"],
function=utils.reshape_ra,
),
iterfield=[
"run_info", "functional_file", "outlier_file", "contrast_entities"
],
name="reshape_rapidart",
)
mean_img = pe.MapNode(
fsl.ImageMaths(output_type="NIFTI_GZ",
op_string="-Tmean",
suffix="_mean"),
iterfield=["in_file", "mask_file"],
name="smooth_susan_avgimg",
)
median_img = pe.MapNode(
fsl.ImageStats(output_type="NIFTI_GZ", op_string="-k %s -p 50"),
iterfield=["in_file", "mask_file"],
name="smooth_susan_medimg",
)
merge = pe.Node(Merge(2, axis="hstack"), name="smooth_merge")
run_susan = pe.MapNode(
fsl.SUSAN(output_type="NIFTI_GZ"),
iterfield=["in_file", "brightness_threshold", "usans"],
name="smooth_susan",
)
mask_functional = pe.MapNode(ApplyMask(),
iterfield=["in_file", "mask_file"],
name="mask_functional")
# Exists solely to correct undesirable behavior of FSL
# that results in loss of constant columns
correct_matrices = pe.MapNode(
Function(
input_names=["design_matrix"],
output_names=["design_matrix"],
function=utils.correct_matrix,
),
iterfield=["design_matrix"],
run_without_submitting=True,
name=f"correct_{level}_matrices",
)
collate = pe.Node(
MergeAll(
fields=[
"effect_maps",
"variance_maps",
"zscore_maps",
"pvalue_maps",
"tstat_maps",
"contrast_metadata",
],
check_lengths=True,
),
name=f"collate_{level}",
)
collate_outputs = pe.Node(
CollateWithMetadata(
fields=[
"effect_maps", "variance_maps", "zscore_maps", "pvalue_maps",
"tstat_maps"
],
field_to_metadata_map={
"effect_maps": {
"stat": "effect"
},
"variance_maps": {
"stat": "variance"
},
"zscore_maps": {
"stat": "z"
},
"pvalue_maps": {
"stat": "p"
},
"tstat_maps": {
"stat": "t"
},
},
),
name=f"collate_{level}_outputs",
)
plot_matrices = pe.MapNode(
PlotMatrices(output_dir=output_dir, database_path=database_path),
iterfield=["mat_file", "con_file", "entities", "run_info"],
run_without_submitting=True,
name=f"plot_{level}_matrices",
)
ds_contrast_maps = pe.MapNode(
BIDSDataSink(base_directory=output_dir, path_patterns=image_pattern),
iterfield=["entities", "in_file"],
run_without_submitting=True,
name=f"ds_{level}_contrast_maps",
)
wrangle_outputs = pe.Node(
IdentityInterface(fields=["contrast_metadata", "contrast_maps"]),
name=f"wrangle_{level}_outputs",
)
# Setup connections among nodes
workflow.connect([(
getter,
get_info,
[
("metadata_files", "metadata_file"),
("events_files", "events_file"),
("regressor_files", "regressor_file"),
("entities", "entities"),
],
)])
if align_volumes and despike:
workflow.connect([
(getter, despiker, [("functional_files", "in_file")]),
(despiker, realign_runs, [("out_file", "in_file")]),
(getter, realign_runs, [("reference_files", "ref_file")]),
(
realign_runs,
wrangle_volumes,
[("out_file", "functional_file")],
),
])
elif align_volumes and not despike:
workflow.connect([
(
getter,
realign_runs,
[("functional_files", "in_file"),
("reference_files", "ref_file")],
),
(
realign_runs,
wrangle_volumes,
[("out_file", "functional_file")],
),
])
elif despike:
workflow.connect([
(getter, despiker, [("functional_files", "in_file")]),
(despiker, wrangle_volumes, [("out_file", "functional_file")]),
])
else:
workflow.connect([(getter, wrangle_volumes, [("functional_files",
"functional_file")])])
if use_rapidart:
workflow.connect([
(get_info, run_rapidart, [("motion_parameters",
"realignment_parameters")]),
(getter, run_rapidart, [("mask_files", "mask_file")]),
(
wrangle_volumes,
run_rapidart,
[("functional_file", "realigned_files")],
),
(
run_rapidart,
reshape_rapidart,
[("outlier_files", "outlier_file")],
),
(
get_info,
reshape_rapidart,
[("run_info", "run_info"),
("contrast_entities", "contrast_entities")],
),
(wrangle_volumes, reshape_rapidart, [("functional_file",
"functional_file")]),
(
reshape_rapidart,
specify_model,
[("run_info", "subject_info")],
),
(reshape_rapidart, plot_matrices, [("run_info", "run_info")]),
(reshape_rapidart, collate, [("contrast_entities",
"contrast_metadata")]),
])
else:
workflow.connect([
(get_info, specify_model, [("run_info", "subject_info")]),
(get_info, plot_matrices, [("run_info", "run_info")]),
(
get_info,
collate,
[("contrast_entities", "contrast_metadata")],
),
])
if smoothing_level == "l1" or smoothing_level == "run":
run_susan.inputs.fwhm = smoothing_fwhm
run_susan.inputs.dimension = dimensionality
estimate_model.inputs.mask_size = smoothing_fwhm
workflow.connect([
(wrangle_volumes, mean_img, [("functional_file", "in_file")]),
(
wrangle_volumes,
median_img,
[("functional_file", "in_file")],
),
(getter, mean_img, [("mask_files", "mask_file")]),
(getter, median_img, [("mask_files", "mask_file")]),
(mean_img, merge, [("out_file", "in1")]),
(median_img, merge, [("out_stat", "in2")]),
(wrangle_volumes, run_susan, [("functional_file", "in_file")]),
(
median_img,
run_susan,
[(
("out_stat", utils.get_btthresh),
"brightness_threshold",
)],
),
(merge, run_susan, [(("out", utils.get_usans), "usans")]),
(getter, mask_functional, [("mask_files", "mask_file")]),
(run_susan, mask_functional, [("smoothed_file", "in_file")]),
(
mask_functional,
specify_model,
[("out_file", "functional_runs")],
),
(
mask_functional,
fit_model,
[("out_file", "functional_data")],
),
])
else:
workflow.connect([
(getter, mask_functional, [("mask_files", "mask_file")]),
(
wrangle_volumes,
mask_functional,
[("functional_file", "in_file")],
),
(
mask_functional,
specify_model,
[("out_file", "functional_runs")],
),
(
mask_functional,
fit_model,
[("out_file", "functional_data")],
),
])
workflow.connect([
(
get_info,
specify_model,
[("repetition_time", "time_repetition")],
),
(specify_model, fit_model, [("session_info", "session_info")]),
(
get_info,
fit_model,
[("repetition_time", "interscan_interval"),
("run_contrasts", "contrasts")],
),
(
fit_model,
first_level_design,
[
("interscan_interval", "interscan_interval"),
("session_info", "session_info"),
("contrasts", "contrasts"),
],
),
(first_level_design, generate_model, [("fsf_files", "fsf_file")]),
(first_level_design, generate_model, [("ev_files", "ev_files")]),
])
if detrend_poly:
workflow.connect([
(
generate_model,
correct_matrices,
[("design_file", "design_matrix")],
),
(
correct_matrices,
plot_matrices,
[("design_matrix", "mat_file")],
),
(
correct_matrices,
estimate_model,
[("design_matrix", "design_file")],
),
])
else:
workflow.connect([
(generate_model, plot_matrices, [("design_file", "mat_file")]),
(
generate_model,
estimate_model,
[("design_file", "design_file")],
),
])
workflow.connect([
(getter, plot_matrices, [("entities", "entities")]),
(generate_model, plot_matrices, [("con_file", "con_file")]),
(fit_model, estimate_model, [("functional_data", "in_file")]),
(generate_model, estimate_model, [("con_file", "tcon_file")]),
(
estimate_model,
calculate_p,
[(("zstats", utils.flatten), "in_file")],
),
(
estimate_model,
collate,
[
("copes", "effect_maps"),
("varcopes", "variance_maps"),
("zstats", "zscore_maps"),
("tstats", "tstat_maps"),
],
),
(calculate_p, collate, [("out_file", "pvalue_maps")]),
(
collate,
collate_outputs,
[
("effect_maps", "effect_maps"),
("variance_maps", "variance_maps"),
("zscore_maps", "zscore_maps"),
("pvalue_maps", "pvalue_maps"),
("tstat_maps", "tstat_maps"),
("contrast_metadata", "metadata"),
],
),
(
collate_outputs,
ds_contrast_maps,
[("out", "in_file"), ("metadata", "entities")],
),
(
collate_outputs,
wrangle_outputs,
[("metadata", "contrast_metadata"), ("out", "contrast_maps")],
),
])
return workflow
def model_fitting(source_img, prepped_img, subject_info, aroma, task, args,
mask_file, run_number):
# Get the necessary parameters
outputdir = args.outputdir
fwhm = args.fwhm
cthresh = args.cthresh
alpha = args.alpha
# Make a task directory in the output folder
if run_number > 0:
taskdir = os.path.join(outputdir,
task + "_run-0" + str(run_number + 1))
else:
taskdir = os.path.join(outputdir, task)
if not os.path.exists(taskdir):
os.mkdir(taskdir)
os.mkdir(os.path.join(taskdir, 'stats'))
os.mkdir(os.path.join(taskdir, 'figs'))
processed_image = preprocess(aroma, fwhm, prepped_img, mask_file, taskdir,
task)
task_vs_baseline = [
task + " vs baseline", 'T', [task, 'baseline'], [1, -1]
] # set up contrasts
contrasts = [task_vs_baseline]
"""
Model fitting workflow
Inputs::
inputspec.session_info : info generated by modelgen.SpecifyModel
inputspec.interscan_interval : interscan interval
inputspec.contrasts : list of contrasts
inputspec.film_threshold : image threshold for FILM estimation
inputspec.model_serial_correlations
inputspec.bases
Outputs::
outputspec.copes
outputspec.varcopes
outputspec.dof_file
outputspec.zfiles
outputspec.parameter_estimates
"""
modelfit = pe.Workflow(name='modelfit', base_dir=taskdir)
modelspec = pe.Node(interface=model.SpecifyModel(),
name="modelspec") # generate design info
inputspec = pe.Node(util.IdentityInterface(fields=[
'session_info', 'interscan_interval', 'contrasts', 'film_threshold',
'functional_data', 'bases', 'model_serial_correlations'
]),
name='inputspec')
level1design = pe.Node(interface=fsl.Level1Design(), name="level1design")
modelgen = pe.MapNode(interface=fsl.FEATModel(),
name='modelgen',
iterfield=['fsf_file', 'ev_files'])
modelestimate = pe.MapNode(
interface=fsl.FILMGLS(smooth_autocorr=True, mask_size=5),
name='modelestimate',
iterfield=['design_file', 'in_file', 'tcon_file'])
merge_contrasts = pe.MapNode(interface=util.Merge(2),
name='merge_contrasts',
iterfield=['in1'])
outputspec = pe.Node(util.IdentityInterface(fields=[
'copes', 'varcopes', 'dof_file', 'zfiles', 'parameter_estimates'
]),
name='outputspec')
modelfit.connect([
(modelspec, inputspec, [('session_info', 'session_info')]),
(inputspec, level1design,
[('interscan_interval', 'interscan_interval'),
('session_info', 'session_info'), ('contrasts', 'contrasts'),
('bases', 'bases'),
('model_serial_correlations', 'model_serial_correlations')]),
(inputspec, modelestimate, [('film_threshold', 'threshold'),
('functional_data', 'in_file')]),
(level1design, modelgen, [('fsf_files', 'fsf_file'),
('ev_files', 'ev_files')]),
(modelgen, modelestimate, [('design_file', 'design_file')]),
(merge_contrasts, outputspec, [('out', 'zfiles')]),
(modelestimate, outputspec, [('param_estimates',
'parameter_estimates'),
('dof_file', 'dof_file')]),
])
modelfit.connect([
(modelgen, modelestimate, [('con_file', 'tcon_file'),
('fcon_file', 'fcon_file')]),
(modelestimate, merge_contrasts, [('zstats', 'in1'),
('zfstats', 'in2')]),
(modelestimate, outputspec, [('copes', 'copes'),
('varcopes', 'varcopes')]),
])
# Define inputs to workflow
modelspec.inputs.functional_runs = processed_image
inputspec.inputs.functional_data = processed_image
modelspec.inputs.subject_info = subject_info
modelspec.inputs.input_units = 'secs'
modelspec.inputs.time_repetition = source_img.entities['RepetitionTime']
modelspec.inputs.high_pass_filter_cutoff = 90
inputspec.inputs.model_serial_correlations = True
inputspec.inputs.film_threshold = 10.0
inputspec.inputs.interscan_interval = source_img.entities['RepetitionTime']
inputspec.inputs.bases = {
'gamma': {
'gammasigma': 3,
'gammadelay': 6,
'derivs': True
}
}
inputspec.inputs.contrasts = contrasts
# Run the model-fitting pipeline. Main outputs are a feat directory (w/ functional img) and a design.mat file
res = modelfit.run()
# outputs
output_txt = open(os.path.join(taskdir, task + '_outputs.txt'), 'w')
print_outputs(output_txt, res)
# The third node, FILM's, first element (i.e. only element) of its 'zstats' output
z_img = list(res.nodes)[2].result.outputs.zstats[0]
# Use False Discovery Rate theory to correct for multiple comparisons
fdr_thresh_img, fdr_threshold = thresholding.map_threshold(
stat_img=z_img,
mask_img=mask_file,
alpha=alpha,
height_control='fdr',
cluster_threshold=cthresh)
print("Thresholding at FDR corrected threshold of " + str(fdr_threshold))
fdr_thresh_img_path = os.path.join(taskdir,
task + '_fdr_thresholded_z.nii.gz')
nibabel.save(fdr_thresh_img, fdr_thresh_img_path)
# Do a cluster analysis using the FDR corrected threshold on the original z_img
print("Performing cluster analysis.")
cl = fsl.Cluster(in_file=z_img, threshold=fdr_threshold)
cluster_file = os.path.join(taskdir, 'stats', task + "_cluster_stats.txt")
cluster_analysis(cluster_file, cl)
# Resample the result image with AFNI
resample_fdr_thresh_img_path = os.path.join(
taskdir, task + '_fdr_thresholded_z_resample.nii.gz')
print("Resampling thresholded image to MNI space")
resample = afni.Resample(master=template,
out_file=resample_fdr_thresh_img_path,
in_file=fdr_thresh_img_path)
resample.run()
os.remove(fdr_thresh_img_path)
print("Image to be returned: " + resample_fdr_thresh_img_path)
return resample_fdr_thresh_img_path
def create_nuisance_modelfit_workflow(name='modelfit', f_contrasts=False):
"""
Create an FSL modelfitting workflow that returns also
residual4d and sigmasquareds.
Example
-------
# >>> modelfit = create_modelfit_workflow()
# >>> modelfit.base_dir = '.'
# >>> info = dict()
# >>> modelfit.inputs.inputspec.session_info = info
# >>> modelfit.inputs.inputspec.interscan_interval = 3.
# >>> modelfit.inputs.inputspec.film_threshold = 1000
# >>> modelfit.run() #doctest: +SKIP
Inputs::
inputspec.session_info : info generated by modelgen.SpecifyModel
inputspec.interscan_interval : interscan interval
inputspec.contrasts : list of contrasts
inputspec.film_threshold : image threshold for FILM estimation
inputspec.model_serial_correlations
inputspec.bases
Outputs::
outputspec.copes
outputspec.varcopes
outputspec.dof_file
outputspec.pfiles
outputspec.zfiles
outputspec.parameter_estimates
outputspec.residual4d
outputspec.sigmasquareds
"""
version = 0
if fsl.Info.version() and \
LooseVersion(fsl.Info.version()) > LooseVersion('5.0.6'):
version = 507
modelfit = pe.Workflow(name=name)
"""
Create the nodes
"""
inputspec = pe.Node(util.IdentityInterface(fields=[
'session_info', 'interscan_interval', 'contrasts', 'film_threshold',
'functional_data', 'bases', 'model_serial_correlations'
]),
name='inputspec')
level1design = pe.Node(interface=fsl.Level1Design(), name="level1design")
modelgen = pe.MapNode(interface=fsl.FEATModel(),
name='modelgen',
iterfield=['fsf_file', 'ev_files'])
if version < 507:
modelestimate = pe.MapNode(interface=fsl.FILMGLS(smooth_autocorr=True,
mask_size=5),
name='modelestimate',
iterfield=['design_file', 'in_file'])
else:
if f_contrasts:
iterfield = ['design_file', 'in_file', 'tcon_file', 'fcon_file']
else:
iterfield = ['design_file', 'in_file', 'tcon_file']
modelestimate = pe.MapNode(interface=fsl.FILMGLS(smooth_autocorr=True,
mask_size=5),
name='modelestimate',
iterfield=iterfield)
if version < 507:
if f_contrasts:
iterfield = [
'tcon_file', 'fcon_file', 'param_estimates', 'sigmasquareds',
'corrections', 'dof_file'
]
else:
iterfield = [
'tcon_file', 'param_estimates', 'sigmasquareds', 'corrections',
'dof_file'
]
conestimate = pe.MapNode(interface=fsl.ContrastMgr(),
name='conestimate',
iterfield=[
'tcon_file', 'fcon_file',
'param_estimates', 'sigmasquareds',
'corrections', 'dof_file'
])
if f_contrasts:
iterfield = ['in1', 'in2']
else:
iterfield = ['in1']
merge_contrasts = pe.MapNode(interface=util.Merge(2),
name='merge_contrasts',
iterfield=iterfield)
ztopval = pe.MapNode(interface=fsl.ImageMaths(op_string='-ztop',
suffix='_pval'),
nested=True,
name='ztop',
iterfield=['in_file'])
outputspec = pe.Node(util.IdentityInterface(fields=[
'copes', 'varcopes', 'dof_file', 'pfiles', 'zfiles',
'parameter_estimates', 'residual4d', 'sigmasquareds'
]),
name='outputspec')
"""
Setup the connections
"""
modelfit.connect([
(inputspec, level1design,
[('interscan_interval', 'interscan_interval'),
('session_info', 'session_info'), ('contrasts', 'contrasts'),
('bases', 'bases'),
('model_serial_correlations', 'model_serial_correlations')]),
(inputspec, modelestimate, [('film_threshold', 'threshold'),
('functional_data', 'in_file')]),
(level1design, modelgen, [('fsf_files', 'fsf_file'),
('ev_files', 'ev_files')]),
(modelgen, modelestimate, [('design_file', 'design_file')]),
# connect also residual4d and sigmasquared
(modelestimate, outputspec, [('param_estimates',
'parameter_estimates'),
('dof_file', 'dof_file'),
('residual4d', 'residual4d'),
('sigmasquareds', 'sigmasquareds')]),
])
if version < 507:
modelfit.connect([
(modelgen, conestimate, [('con_file', 'tcon_file'),
('fcon_file', 'fcon_file')]),
(modelestimate, conestimate, [('param_estimates',
'param_estimates'),
('sigmasquareds', 'sigmasquareds'),
('corrections', 'corrections'),
('dof_file', 'dof_file')]),
(conestimate, outputspec, [('copes', 'copes'),
('varcopes', 'varcopes')]),
])
else:
modelfit.connect([
(modelgen, modelestimate, [('con_file', 'tcon_file'),
('fcon_file', 'fcon_file')]),
(modelestimate, outputspec, [('copes', 'copes'),
('varcopes', 'varcopes')]),
])
return modelfit
#Wraps command **fslmaths**
NodeHash_43b01b0 = pe.Node(interface=fsl.ApplyMask(), name='NodeName_43b01b0')
#Custom interface wrapping function Tsv2subjectinfo
NodeHash_3042f20 = pe.Node(interface=firstlevelhelpers.Tsv2subjectinfo,
name='NodeName_3042f20')
#Makes a model specification compatible with spm/fsl designers.
NodeHash_6bef320 = pe.Node(interface=modelgen.SpecifyModel(),
name='NodeName_6bef320')
NodeHash_6bef320.inputs.high_pass_filter_cutoff = 0
NodeHash_6bef320.inputs.input_units = 'secs'
NodeHash_6bef320.inputs.time_repetition = 2.0
#Generate FEAT specific files
NodeHash_8241250 = pe.Node(interface=fsl.Level1Design(),
name='NodeName_8241250')
NodeHash_8241250.inputs.bases = {'dgamma': {'derivs': False}}
NodeHash_8241250.inputs.contrasts = [
('con-incon', 'T', ['congruent_correct', 'congruent_correct'], [-1, 1])
]
NodeHash_8241250.inputs.interscan_interval = 2.0
NodeHash_8241250.inputs.model_serial_correlations = True
#Wraps command **feat_model**
NodeHash_8b12580 = pe.Node(interface=fsl.FEATModel(), name='NodeName_8b12580')
#Wraps command **film_gls**
NodeHash_5015c80 = pe.Node(interface=fsl.FILMGLS(), name='NodeName_5015c80')
#Generic datasink module to store structured outputs
def first_level_wf(in_files, output_dir, fwhm=6.0, name='wf_1st_level'):
workflow = pe.Workflow(name=name)
datasource = pe.Node(niu.Function(function=_dict_ds,
output_names=DATA_ITEMS),
name='datasource')
datasource.inputs.in_dict = in_files
datasource.iterables = ('sub', sorted(in_files.keys()))
# Extract motion parameters from regressors file
runinfo = pe.Node(niu.Function(input_names=[
'in_file', 'events_file', 'regressors_file', 'regressors_names'
],
function=_bids2nipypeinfo,
output_names=['info', 'realign_file']),
name='runinfo')
# Set the column names to be used from the confounds file
runinfo.inputs.regressors_names = ['dvars', 'framewise_displacement'] + \
['a_comp_cor_%02d' % i for i in range(6)] + ['cosine%02d' % i for i in range(4)]
# SUSAN smoothing
susan = create_susan_smooth()
susan.inputs.inputnode.fwhm = fwhm
l1_spec = pe.Node(SpecifyModel(parameter_source='FSL',
input_units='secs',
high_pass_filter_cutoff=100),
name='l1_spec')
# l1_model creates a first-level model design
l1_model = pe.Node(
fsl.Level1Design(
bases={'dgamma': {
'derivs': True
}},
model_serial_correlations=True,
#ENTER YOUR OWN CONTRAST HERE
contrasts=[],
# orthogonalization=orthogonality,
),
name='l1_model')
# feat_spec generates an fsf model specification file
feat_spec = pe.Node(fsl.FEATModel(), name='feat_spec')
# feat_fit actually runs FEAT
feat_fit = pe.Node(fsl.FEAT(), name='feat_fit', mem_gb=12)
feat_select = pe.Node(nio.SelectFiles({
'cope': 'stats/cope1.nii.gz',
'pe': 'stats/pe[0-9][0-9].nii.gz',
'tstat': 'stats/tstat1.nii.gz',
'varcope': 'stats/varcope1.nii.gz',
'zstat': 'stats/zstat1.nii.gz',
}),
name='feat_select')
ds_cope = pe.Node(DerivativesDataSink(base_directory=str(output_dir),
keep_dtype=False,
suffix='cope',
desc='intask'),
name='ds_cope',
run_without_submitting=True)
ds_varcope = pe.Node(DerivativesDataSink(base_directory=str(output_dir),
keep_dtype=False,
suffix='varcope',
desc='intask'),
name='ds_varcope',
run_without_submitting=True)
ds_zstat = pe.Node(DerivativesDataSink(base_directory=str(output_dir),
keep_dtype=False,
suffix='zstat',
desc='intask'),
name='ds_zstat',
run_without_submitting=True)
ds_tstat = pe.Node(DerivativesDataSink(base_directory=str(output_dir),
keep_dtype=False,
suffix='tstat',
desc='intask'),
name='ds_tstat',
run_without_submitting=True)
workflow.connect([
(datasource, susan, [('bold', 'inputnode.in_files'),
('mask', 'inputnode.mask_file')]),
(datasource, runinfo, [('events', 'events_file'),
('regressors', 'regressors_file')]),
(susan, l1_spec, [('outputnode.smoothed_files', 'functional_runs')]),
(datasource, l1_spec, [('tr', 'time_repetition')]),
(datasource, l1_model, [('tr', 'interscan_interval')]),
(datasource, ds_cope, [('bold', 'source_file')]),
(datasource, ds_varcope, [('bold', 'source_file')]),
(datasource, ds_zstat, [('bold', 'source_file')]),
(datasource, ds_tstat, [('bold', 'source_file')]),
(susan, runinfo, [('outputnode.smoothed_files', 'in_file')]),
(runinfo, l1_spec, [('info', 'subject_info'),
('realign_file', 'realignment_parameters')]),
(l1_spec, l1_model, [('session_info', 'session_info')]),
(l1_model, feat_spec, [('fsf_files', 'fsf_file'),
('ev_files', 'ev_files')]),
(l1_model, feat_fit, [('fsf_files', 'fsf_file')]),
(feat_fit, feat_select, [('feat_dir', 'base_directory')]),
(feat_select, ds_cope, [('cope', 'in_file')]),
(feat_select, ds_varcope, [('varcope', 'in_file')]),
(feat_select, ds_zstat, [('zstat', 'in_file')]),
(feat_select, ds_tstat, [('tstat', 'in_file')]),
])
return workflow
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
#Set up model fitting workflow (we assume data has been preprocessed with fmriprep)
modelfit = pe.Workflow(name='modelfit')
#Custom interface wrapping function Tsv2subjectinfo
tsv2subjinfo = pe.MapNode(util.Function(
function=utils.tsv2subjectinfo,
input_names=['events_file', 'exclude', 'confounds_file', 'trim_indices'],
output_names=['subject_info']),
name="tsv2subjinfo",
iterfield=['events_file', 'confounds_file'])
modelspec = pe.MapNode(interface=model.SpecifyModel(),
name="modelspec",
iterfield=['subject_info'])
level1design = pe.MapNode(interface=fsl.Level1Design(),
name="level1design",
iterfield=['session_info'])
modelgen = pe.MapNode(interface=fsl.FEATModel(),
name='modelgen',
iterfield=["fsf_file", "ev_files"])
trim = pe.MapNode(interface=Trim(), name="trim", iterfield=['in_file'])
applymask = pe.MapNode(interface=fsl.ApplyMask(),
name="applymask",
iterfield=["in_file", "mask_file"])
modelestimate = pe.MapNode(interface=fsl.FILMGLS(),
name='modelestimate',
iterfield=['design_file', 'in_file', 'tcon_file'])
Use :class:`nipype.algorithms.modelgen.SpecifyModel` to generate design information.
"""
modelspec = pe.Node(interface=model.SpecifyModel(),
name="modelspec")
modelspec.inputs.input_units = 'secs'
modelspec.inputs.time_repetition = tr
modelspec.inputs.high_pass_filter_cutoff= 120
"""
Use :class:`nipype.interfaces.fsl.Level1Design` to generate a run specific fsf
file for analysis
"""
## Building contrasts
level1design = pe.Node(interface=fsl.Level1Design(), name="level1design")
cont1 = ['Trauma1_0>Sad1_0', 'T', ['trauma1_0', 'sad1_0'], [1, -1]]
cont2 = ['Trauma1_0>Relax1_0', 'T', ['trauma1_0', 'relax1_0'], [1, -1]]
cont3 = ['Sad1_0>Relax1_0', 'T', ['sad1_0', 'relax1_0'], [1, -1]]
cont4 = ['trauma1_0 > trauma2_0', 'T', ['trauma1_0', 'trauma2_0'], [1, -1]]
cont5 = ['Trauma1_0>Trauma1_2_3', 'T', ['trauma1_0', 'trauma1_2','trauma1_3'], [1, -0.5, -0.5]]
cont6 = ['Trauma1 > Trauma2', 'T', ['trauma1_0', 'trauma1_1', 'trauma1_2', 'trauma1_3', 'trauma2_0', 'trauma2_1', 'trauma2_2', 'trauma2_3'], [0.25, 0.25, 0.25, 0.25, -0.25, -0.25, -0.25, -0.25 ]]
cont7 = ['Trauma1_01>relax1_01', 'T', ['trauma1_0', 'trauma1_1', 'relax1_0', 'relax1_1'], [0.5,0.5,-0.5,-0.5]]
contrasts = [cont1, cont2, cont3, cont4, cont5, cont6, cont7]
level1design.inputs.interscan_interval = tr
level1design.inputs.bases = {'dgamma': {'derivs': False}}
level1design.inputs.contrasts = contrasts
level1design.inputs.model_serial_correlations = True
"""
#
l1_spec = pe.Node(SpecifyModel(
parameter_source='FSL',
input_units='secs',
high_pass_filter_cutoff=120,
time_repetition=tr,
),
name='l1_spec')
# l1_model creates a first-level model design
l1_model = pe.Node(
fsl.Level1Design(
bases={'dgamma': {
'derivs': True
}}, # adding temporal derivative of double gamma
model_serial_correlations=True,
interscan_interval=tr,
contrasts=contrasts
# orthogonalization=orthogonality,
),
name='l1_model')
# feat_spec generates an fsf model specification file
feat_spec = pe.Node(fsl.FEATModel(), name='feat_spec')
# feat_fit actually runs FEAT
feat_fit = pe.Node(fsl.FEAT(), name='feat_fit', mem_gb=5)
# instead of FEAT
# modelestimate = pe.MapNode(interface=fsl.FILMGLS(smooth_autocorr=True,
# mask_size=5,