def analyze_openfmri_dataset(data_dir, subject=None, model_id=None,
task_id=None, output_dir=None, subj_prefix='*'):
"""Analyzes an open fmri dataset
Parameters
----------
data_dir : str
Path to the base data directory
work_dir : str
Nipype working directory (defaults to cwd)
"""
"""
Load nipype workflows
"""
preproc = create_featreg_preproc(whichvol='first')
modelfit = create_modelfit_workflow()
fixed_fx = create_fixed_effects_flow()
registration = create_reg_workflow()
"""
Remove the plotting connection so that plot iterables don't propagate
to the model stage
"""
preproc.disconnect(preproc.get_node('plot_motion'), 'out_file',
preproc.get_node('outputspec'), 'motion_plots')
"""
Set up openfmri data specific components
"""
subjects = sorted([path.split(os.path.sep)[-1] for path in
glob(os.path.join(data_dir, subj_prefix))])
infosource = pe.Node(niu.IdentityInterface(fields=['subject_id',
'model_id',
'task_id']),
name='infosource')
if len(subject) == 0:
infosource.iterables = [('subject_id', subjects),
('model_id', [model_id]),
('task_id', task_id)]
else:
infosource.iterables = [('subject_id',
[subjects[subjects.index(subj)] for subj in subject]),
('model_id', [model_id]),
('task_id', task_id)]
subjinfo = pe.Node(niu.Function(input_names=['subject_id', 'base_dir',
'task_id', 'model_id'],
output_names=['run_id', 'conds', 'TR'],
function=get_subjectinfo),
name='subjectinfo')
subjinfo.inputs.base_dir = data_dir
"""
Return data components as anat, bold and behav
"""
datasource = pe.Node(nio.DataGrabber(infields=['subject_id', 'run_id',
'task_id', 'model_id'],
outfields=['anat', 'bold', 'behav',
'contrasts']),
name='datasource')
datasource.inputs.base_directory = data_dir
datasource.inputs.template = '*'
datasource.inputs.field_template = {'anat': '%s/anatomy/T1_001.nii.gz',
'bold': '%s/BOLD/task%03d_r*/bold.nii.gz',
'behav': ('%s/model/model%03d/onsets/task%03d_'
'run%03d/cond*.txt'),
'contrasts': ('models/model%03d/'
'task_contrasts.txt')}
datasource.inputs.template_args = {'anat': [['subject_id']],
'bold': [['subject_id', 'task_id']],
'behav': [['subject_id', 'model_id',
'task_id', 'run_id']],
'contrasts': [['model_id']]}
datasource.inputs.sort_filelist = True
"""
Create meta workflow
"""
wf = pe.Workflow(name='openfmri')
wf.connect(infosource, 'subject_id', subjinfo, 'subject_id')
wf.connect(infosource, 'model_id', subjinfo, 'model_id')
wf.connect(infosource, 'task_id', subjinfo, 'task_id')
wf.connect(infosource, 'subject_id', datasource, 'subject_id')
wf.connect(infosource, 'model_id', datasource, 'model_id')
wf.connect(infosource, 'task_id', datasource, 'task_id')
wf.connect(subjinfo, 'run_id', datasource, 'run_id')
wf.connect([(datasource, preproc, [('bold', 'inputspec.func')]),
])
def get_highpass(TR, hpcutoff):
return hpcutoff / (2 * TR)
gethighpass = pe.Node(niu.Function(input_names=['TR', 'hpcutoff'],
output_names=['highpass'],
function=get_highpass),
name='gethighpass')
wf.connect(subjinfo, 'TR', gethighpass, 'TR')
wf.connect(gethighpass, 'highpass', preproc, 'inputspec.highpass')
"""
Setup a basic set of contrasts, a t-test per condition
"""
def get_contrasts(contrast_file, task_id, conds):
import numpy as np
contrast_def = np.genfromtxt(contrast_file, dtype=object)
if len(contrast_def.shape) == 1:
contrast_def = contrast_def[None, :]
contrasts = []
for row in contrast_def:
if row[0] != 'task%03d' % task_id:
continue
con = [row[1], 'T', ['cond%03d' % (i + 1) for i in range(len(conds))],
row[2:].astype(float).tolist()]
contrasts.append(con)
# add auto contrasts for each column
for i, cond in enumerate(conds):
con = [cond, 'T', ['cond%03d' % (i + 1)], [1]]
contrasts.append(con)
return contrasts
contrastgen = pe.Node(niu.Function(input_names=['contrast_file',
'task_id', 'conds'],
output_names=['contrasts'],
function=get_contrasts),
name='contrastgen')
art = pe.MapNode(interface=ra.ArtifactDetect(use_differences=[True, False],
use_norm=True,
norm_threshold=1,
zintensity_threshold=3,
parameter_source='FSL',
mask_type='file'),
iterfield=['realigned_files', 'realignment_parameters',
'mask_file'],
name="art")
modelspec = pe.Node(interface=model.SpecifyModel(),
name="modelspec")
modelspec.inputs.input_units = 'secs'
def check_behav_list(behav):
out_behav = []
if isinstance(behav, six.string_types):
behav = [behav]
for val in behav:
if not isinstance(val, list):
out_behav.append([val])
else:
out_behav.append(val)
return out_behav
wf.connect(subjinfo, 'TR', modelspec, 'time_repetition')
wf.connect(datasource, ('behav', check_behav_list), modelspec, 'event_files')
wf.connect(subjinfo, 'TR', modelfit, 'inputspec.interscan_interval')
wf.connect(subjinfo, 'conds', contrastgen, 'conds')
wf.connect(datasource, 'contrasts', contrastgen, 'contrast_file')
wf.connect(infosource, 'task_id', contrastgen, 'task_id')
wf.connect(contrastgen, 'contrasts', modelfit, 'inputspec.contrasts')
wf.connect([(preproc, art, [('outputspec.motion_parameters',
'realignment_parameters'),
('outputspec.realigned_files',
'realigned_files'),
('outputspec.mask', 'mask_file')]),
(preproc, modelspec, [('outputspec.highpassed_files',
'functional_runs'),
('outputspec.motion_parameters',
'realignment_parameters')]),
(art, modelspec, [('outlier_files', 'outlier_files')]),
(modelspec, modelfit, [('session_info',
'inputspec.session_info')]),
(preproc, modelfit, [('outputspec.highpassed_files',
'inputspec.functional_data')])
])
"""
Reorder the copes so that now it combines across runs
"""
def sort_copes(files):
numelements = len(files[0])
outfiles = []
for i in range(numelements):
outfiles.insert(i, [])
for j, elements in enumerate(files):
outfiles[i].append(elements[i])
return outfiles
def num_copes(files):
return len(files)
pickfirst = lambda x: x[0]
wf.connect([(preproc, fixed_fx, [(('outputspec.mask', pickfirst),
'flameo.mask_file')]),
(modelfit, fixed_fx, [(('outputspec.copes', sort_copes),
'inputspec.copes'),
('outputspec.dof_file',
'inputspec.dof_files'),
(('outputspec.varcopes',
sort_copes),
'inputspec.varcopes'),
(('outputspec.copes', num_copes),
'l2model.num_copes'),
])
])
wf.connect(preproc, 'outputspec.mean', registration, 'inputspec.mean_image')
wf.connect(datasource, 'anat', registration, 'inputspec.anatomical_image')
registration.inputs.inputspec.target_image = fsl.Info.standard_image('MNI152_T1_2mm.nii.gz')
registration.inputs.inputspec.target_image_brain = fsl.Info.standard_image('MNI152_T1_2mm_brain.nii.gz')
registration.inputs.inputspec.config_file = 'T1_2_MNI152_2mm'
def merge_files(copes, varcopes, zstats):
out_files = []
splits = []
out_files.extend(copes)
splits.append(len(copes))
out_files.extend(varcopes)
splits.append(len(varcopes))
out_files.extend(zstats)
splits.append(len(zstats))
return out_files, splits
mergefunc = pe.Node(niu.Function(input_names=['copes', 'varcopes',
'zstats'],
output_names=['out_files', 'splits'],
function=merge_files),
name='merge_files')
wf.connect([(fixed_fx.get_node('outputspec'), mergefunc,
[('copes', 'copes'),
('varcopes', 'varcopes'),
('zstats', 'zstats'),
])])
wf.connect(mergefunc, 'out_files', registration, 'inputspec.source_files')
def split_files(in_files, splits):
copes = in_files[:splits[0]]
varcopes = in_files[splits[0]:(splits[0] + splits[1])]
zstats = in_files[(splits[0] + splits[1]):]
return copes, varcopes, zstats
splitfunc = pe.Node(niu.Function(input_names=['in_files', 'splits'],
output_names=['copes', 'varcopes',
'zstats'],
function=split_files),
name='split_files')
wf.connect(mergefunc, 'splits', splitfunc, 'splits')
wf.connect(registration, 'outputspec.transformed_files',
splitfunc, 'in_files')
"""
Connect to a datasink
"""
def get_subs(subject_id, conds, model_id, task_id):
subs = [('_subject_id_%s_' % subject_id, '')]
subs.append(('_model_id_%d' % model_id, 'model%03d' %model_id))
subs.append(('task_id_%d/' % task_id, '/task%03d_' % task_id))
subs.append(('bold_dtype_mcf_mask_smooth_mask_gms_tempfilt_mean_warp',
'mean'))
subs.append(('bold_dtype_mcf_mask_smooth_mask_gms_tempfilt_mean_flirt',
'affine'))
for i in range(len(conds)):
subs.append(('_flameo%d/cope1.' % i, 'cope%02d.' % (i + 1)))
subs.append(('_flameo%d/varcope1.' % i, 'varcope%02d.' % (i + 1)))
subs.append(('_flameo%d/zstat1.' % i, 'zstat%02d.' % (i + 1)))
subs.append(('_flameo%d/tstat1.' % i, 'tstat%02d.' % (i + 1)))
subs.append(('_flameo%d/res4d.' % i, 'res4d%02d.' % (i + 1)))
subs.append(('_warpall%d/cope1_warp.' % i,
'cope%02d.' % (i + 1)))
subs.append(('_warpall%d/varcope1_warp.' % (len(conds) + i),
'varcope%02d.' % (i + 1)))
subs.append(('_warpall%d/zstat1_warp.' % (2 * len(conds) + i),
'zstat%02d.' % (i + 1)))
return subs
subsgen = pe.Node(niu.Function(input_names=['subject_id', 'conds',
'model_id', 'task_id'],
output_names=['substitutions'],
function=get_subs),
name='subsgen')
datasink = pe.Node(interface=nio.DataSink(),
name="datasink")
wf.connect(infosource, 'subject_id', datasink, 'container')
wf.connect(infosource, 'subject_id', subsgen, 'subject_id')
wf.connect(infosource, 'model_id', subsgen, 'model_id')
wf.connect(infosource, 'task_id', subsgen, 'task_id')
wf.connect(contrastgen, 'contrasts', subsgen, 'conds')
wf.connect(subsgen, 'substitutions', datasink, 'substitutions')
wf.connect([(fixed_fx.get_node('outputspec'), datasink,
[('res4d', 'res4d'),
('copes', 'copes'),
('varcopes', 'varcopes'),
('zstats', 'zstats'),
('tstats', 'tstats')])
])
wf.connect([(splitfunc, datasink,
[('copes', 'copes.mni'),
('varcopes', 'varcopes.mni'),
('zstats', 'zstats.mni'),
])])
wf.connect(registration, 'outputspec.transformed_mean', datasink, 'mean.mni')
wf.connect(registration, 'outputspec.func2anat_transform', datasink, 'xfm.mean2anat')
wf.connect(registration, 'outputspec.anat2target_transform', datasink, 'xfm.anat2target')
"""
Set processing parameters
"""
hpcutoff = 120.
preproc.inputs.inputspec.fwhm = 6.0
gethighpass.inputs.hpcutoff = hpcutoff
modelspec.inputs.high_pass_filter_cutoff = hpcutoff
modelfit.inputs.inputspec.bases = {'dgamma': {'derivs': True}}
modelfit.inputs.inputspec.model_serial_correlations = True
modelfit.inputs.inputspec.film_threshold = 1000
datasink.inputs.base_directory = output_dir
return wf
Preliminaries
-------------
Setup any package specific configuration. The output file format for FSL
routines is being set to compressed NIFTI.
"""
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
level1_workflow = pe.Workflow(name='level1flow')
preproc = create_featreg_preproc(whichvol='first')
modelfit = create_modelfit_workflow()
fixed_fx = create_fixed_effects_flow()
"""
Add artifact detection and model specification nodes between the preprocessing
and modelfitting workflows.
"""
art = pe.MapNode(
ra.ArtifactDetect(use_differences=[True, False],
use_norm=True,
norm_threshold=1,
zintensity_threshold=3,
parameter_source='FSL',
mask_type='file'),
iterfield=['realigned_files', 'realignment_parameters', 'mask_file'],
name="art")
def analyze_openfmri_dataset(
data_dir,
subject=None,
model_id=None,
task_id=None,
output_dir=None,
subj_prefix="*",
hpcutoff=120.0,
use_derivatives=True,
fwhm=6.0,
subjects_dir=None,
target=None,
):
"""Analyzes an open fmri dataset
Parameters
----------
data_dir : str
Path to the base data directory
work_dir : str
Nipype working directory (defaults to cwd)
"""
"""
Load nipype workflows
"""
preproc = create_featreg_preproc(whichvol="first")
modelfit = create_modelfit_workflow()
fixed_fx = create_fixed_effects_flow()
if subjects_dir:
registration = create_fs_reg_workflow()
else:
registration = create_reg_workflow()
"""
Remove the plotting connection so that plot iterables don't propagate
to the model stage
"""
preproc.disconnect(preproc.get_node("plot_motion"), "out_file", preproc.get_node("outputspec"), "motion_plots")
"""
Set up openfmri data specific components
"""
subjects = sorted([path.split(os.path.sep)[-1] for path in glob(os.path.join(data_dir, subj_prefix))])
infosource = pe.Node(niu.IdentityInterface(fields=["subject_id", "model_id", "task_id"]), name="infosource")
if len(subject) == 0:
infosource.iterables = [("subject_id", subjects), ("model_id", [model_id]), ("task_id", task_id)]
else:
infosource.iterables = [
("subject_id", [subjects[subjects.index(subj)] for subj in subject]),
("model_id", [model_id]),
("task_id", task_id),
]
subjinfo = pe.Node(
niu.Function(
input_names=["subject_id", "base_dir", "task_id", "model_id"],
output_names=["run_id", "conds", "TR"],
function=get_subjectinfo,
),
name="subjectinfo",
)
subjinfo.inputs.base_dir = data_dir
"""
Return data components as anat, bold and behav
"""
contrast_file = os.path.join(data_dir, "models", "model%03d" % model_id, "task_contrasts.txt")
has_contrast = os.path.exists(contrast_file)
if has_contrast:
datasource = pe.Node(
nio.DataGrabber(
infields=["subject_id", "run_id", "task_id", "model_id"],
outfields=["anat", "bold", "behav", "contrasts"],
),
name="datasource",
)
else:
datasource = pe.Node(
nio.DataGrabber(
infields=["subject_id", "run_id", "task_id", "model_id"], outfields=["anat", "bold", "behav"]
),
name="datasource",
)
datasource.inputs.base_directory = data_dir
datasource.inputs.template = "*"
if has_contrast:
datasource.inputs.field_template = {
"anat": "%s/anatomy/T1_001.nii.gz",
"bold": "%s/BOLD/task%03d_r*/bold.nii.gz",
"behav": ("%s/model/model%03d/onsets/task%03d_" "run%03d/cond*.txt"),
"contrasts": ("models/model%03d/" "task_contrasts.txt"),
}
datasource.inputs.template_args = {
"anat": [["subject_id"]],
"bold": [["subject_id", "task_id"]],
"behav": [["subject_id", "model_id", "task_id", "run_id"]],
"contrasts": [["model_id"]],
}
else:
datasource.inputs.field_template = {
"anat": "%s/anatomy/T1_001.nii.gz",
"bold": "%s/BOLD/task%03d_r*/bold.nii.gz",
"behav": ("%s/model/model%03d/onsets/task%03d_" "run%03d/cond*.txt"),
}
datasource.inputs.template_args = {
"anat": [["subject_id"]],
"bold": [["subject_id", "task_id"]],
"behav": [["subject_id", "model_id", "task_id", "run_id"]],
}
datasource.inputs.sort_filelist = True
"""
Create meta workflow
"""
wf = pe.Workflow(name="openfmri")
wf.connect(infosource, "subject_id", subjinfo, "subject_id")
wf.connect(infosource, "model_id", subjinfo, "model_id")
wf.connect(infosource, "task_id", subjinfo, "task_id")
wf.connect(infosource, "subject_id", datasource, "subject_id")
wf.connect(infosource, "model_id", datasource, "model_id")
wf.connect(infosource, "task_id", datasource, "task_id")
wf.connect(subjinfo, "run_id", datasource, "run_id")
wf.connect([(datasource, preproc, [("bold", "inputspec.func")])])
def get_highpass(TR, hpcutoff):
return hpcutoff / (2 * TR)
gethighpass = pe.Node(
niu.Function(input_names=["TR", "hpcutoff"], output_names=["highpass"], function=get_highpass),
name="gethighpass",
)
wf.connect(subjinfo, "TR", gethighpass, "TR")
wf.connect(gethighpass, "highpass", preproc, "inputspec.highpass")
"""
Setup a basic set of contrasts, a t-test per condition
"""
def get_contrasts(contrast_file, task_id, conds):
import numpy as np
import os
contrast_def = []
if os.path.exists(contrast_file):
with open(contrast_file, "rt") as fp:
contrast_def.extend([np.array(row.split()) for row in fp.readlines() if row.strip()])
contrasts = []
for row in contrast_def:
if row[0] != "task%03d" % task_id:
continue
con = [row[1], "T", ["cond%03d" % (i + 1) for i in range(len(conds))], row[2:].astype(float).tolist()]
contrasts.append(con)
# add auto contrasts for each column
for i, cond in enumerate(conds):
con = [cond, "T", ["cond%03d" % (i + 1)], [1]]
contrasts.append(con)
return contrasts
contrastgen = pe.Node(
niu.Function(
input_names=["contrast_file", "task_id", "conds"], output_names=["contrasts"], function=get_contrasts
),
name="contrastgen",
)
art = pe.MapNode(
interface=ra.ArtifactDetect(
use_differences=[True, False],
use_norm=True,
norm_threshold=1,
zintensity_threshold=3,
parameter_source="FSL",
mask_type="file",
),
iterfield=["realigned_files", "realignment_parameters", "mask_file"],
name="art",
)
modelspec = pe.Node(interface=model.SpecifyModel(), name="modelspec")
modelspec.inputs.input_units = "secs"
def check_behav_list(behav, run_id, conds):
from nipype.external import six
import numpy as np
num_conds = len(conds)
if isinstance(behav, six.string_types):
behav = [behav]
behav_array = np.array(behav).flatten()
num_elements = behav_array.shape[0]
return behav_array.reshape(num_elements / num_conds, num_conds).tolist()
reshape_behav = pe.Node(
niu.Function(input_names=["behav", "run_id", "conds"], output_names=["behav"], function=check_behav_list),
name="reshape_behav",
)
wf.connect(subjinfo, "TR", modelspec, "time_repetition")
wf.connect(datasource, "behav", reshape_behav, "behav")
wf.connect(subjinfo, "run_id", reshape_behav, "run_id")
wf.connect(subjinfo, "conds", reshape_behav, "conds")
wf.connect(reshape_behav, "behav", modelspec, "event_files")
wf.connect(subjinfo, "TR", modelfit, "inputspec.interscan_interval")
wf.connect(subjinfo, "conds", contrastgen, "conds")
if has_contrast:
wf.connect(datasource, "contrasts", contrastgen, "contrast_file")
else:
contrastgen.inputs.contrast_file = ""
wf.connect(infosource, "task_id", contrastgen, "task_id")
wf.connect(contrastgen, "contrasts", modelfit, "inputspec.contrasts")
wf.connect(
[
(
preproc,
art,
[
("outputspec.motion_parameters", "realignment_parameters"),
("outputspec.realigned_files", "realigned_files"),
("outputspec.mask", "mask_file"),
],
),
(
preproc,
modelspec,
[
("outputspec.highpassed_files", "functional_runs"),
("outputspec.motion_parameters", "realignment_parameters"),
],
),
(art, modelspec, [("outlier_files", "outlier_files")]),
(modelspec, modelfit, [("session_info", "inputspec.session_info")]),
(preproc, modelfit, [("outputspec.highpassed_files", "inputspec.functional_data")]),
]
)
# Comute TSNR on realigned data regressing polynomials upto order 2
tsnr = MapNode(TSNR(regress_poly=2), iterfield=["in_file"], name="tsnr")
wf.connect(preproc, "outputspec.realigned_files", tsnr, "in_file")
# Compute the median image across runs
calc_median = Node(
Function(input_names=["in_files"], output_names=["median_file"], function=median, imports=imports),
name="median",
)
wf.connect(tsnr, "detrended_file", calc_median, "in_files")
"""
Reorder the copes so that now it combines across runs
"""
def sort_copes(copes, varcopes, contrasts):
import numpy as np
if not isinstance(copes, list):
copes = [copes]
varcopes = [varcopes]
num_copes = len(contrasts)
n_runs = len(copes)
all_copes = np.array(copes).flatten()
all_varcopes = np.array(varcopes).flatten()
outcopes = all_copes.reshape(len(all_copes) / num_copes, num_copes).T.tolist()
outvarcopes = all_varcopes.reshape(len(all_varcopes) / num_copes, num_copes).T.tolist()
return outcopes, outvarcopes, n_runs
cope_sorter = pe.Node(
niu.Function(
input_names=["copes", "varcopes", "contrasts"],
output_names=["copes", "varcopes", "n_runs"],
function=sort_copes,
),
name="cope_sorter",
)
pickfirst = lambda x: x[0]
wf.connect(contrastgen, "contrasts", cope_sorter, "contrasts")
wf.connect(
[
(preproc, fixed_fx, [(("outputspec.mask", pickfirst), "flameo.mask_file")]),
(modelfit, cope_sorter, [("outputspec.copes", "copes")]),
(modelfit, cope_sorter, [("outputspec.varcopes", "varcopes")]),
(
cope_sorter,
fixed_fx,
[("copes", "inputspec.copes"), ("varcopes", "inputspec.varcopes"), ("n_runs", "l2model.num_copes")],
),
(modelfit, fixed_fx, [("outputspec.dof_file", "inputspec.dof_files")]),
]
)
wf.connect(calc_median, "median_file", registration, "inputspec.mean_image")
if subjects_dir:
wf.connect(infosource, "subject_id", registration, "inputspec.subject_id")
registration.inputs.inputspec.subjects_dir = subjects_dir
registration.inputs.inputspec.target_image = fsl.Info.standard_image("MNI152_T1_2mm_brain.nii.gz")
if target:
registration.inputs.inputspec.target_image = target
else:
wf.connect(datasource, "anat", registration, "inputspec.anatomical_image")
registration.inputs.inputspec.target_image = fsl.Info.standard_image("MNI152_T1_2mm.nii.gz")
registration.inputs.inputspec.target_image_brain = fsl.Info.standard_image("MNI152_T1_2mm_brain.nii.gz")
registration.inputs.inputspec.config_file = "T1_2_MNI152_2mm"
def merge_files(copes, varcopes, zstats):
out_files = []
splits = []
out_files.extend(copes)
splits.append(len(copes))
out_files.extend(varcopes)
splits.append(len(varcopes))
out_files.extend(zstats)
splits.append(len(zstats))
return out_files, splits
mergefunc = pe.Node(
niu.Function(
input_names=["copes", "varcopes", "zstats"], output_names=["out_files", "splits"], function=merge_files
),
name="merge_files",
)
wf.connect(
[
(
fixed_fx.get_node("outputspec"),
mergefunc,
[("copes", "copes"), ("varcopes", "varcopes"), ("zstats", "zstats")],
)
]
)
wf.connect(mergefunc, "out_files", registration, "inputspec.source_files")
def split_files(in_files, splits):
copes = in_files[: splits[0]]
varcopes = in_files[splits[0] : (splits[0] + splits[1])]
zstats = in_files[(splits[0] + splits[1]) :]
return copes, varcopes, zstats
splitfunc = pe.Node(
niu.Function(
input_names=["in_files", "splits"], output_names=["copes", "varcopes", "zstats"], function=split_files
),
name="split_files",
)
wf.connect(mergefunc, "splits", splitfunc, "splits")
wf.connect(registration, "outputspec.transformed_files", splitfunc, "in_files")
if subjects_dir:
get_roi_mean = pe.MapNode(fs.SegStats(default_color_table=True), iterfield=["in_file"], name="get_aparc_means")
get_roi_mean.inputs.avgwf_txt_file = True
wf.connect(fixed_fx.get_node("outputspec"), "copes", get_roi_mean, "in_file")
wf.connect(registration, "outputspec.aparc", get_roi_mean, "segmentation_file")
get_roi_tsnr = pe.MapNode(fs.SegStats(default_color_table=True), iterfield=["in_file"], name="get_aparc_tsnr")
get_roi_tsnr.inputs.avgwf_txt_file = True
wf.connect(tsnr, "tsnr_file", get_roi_tsnr, "in_file")
wf.connect(registration, "outputspec.aparc", get_roi_tsnr, "segmentation_file")
"""
Connect to a datasink
"""
def get_subs(subject_id, conds, run_id, model_id, task_id):
subs = [("_subject_id_%s_" % subject_id, "")]
subs.append(("_model_id_%d" % model_id, "model%03d" % model_id))
subs.append(("task_id_%d/" % task_id, "/task%03d_" % task_id))
subs.append(("bold_dtype_mcf_mask_smooth_mask_gms_tempfilt_mean_warp", "mean"))
subs.append(("bold_dtype_mcf_mask_smooth_mask_gms_tempfilt_mean_flirt", "affine"))
for i in range(len(conds)):
subs.append(("_flameo%d/cope1." % i, "cope%02d." % (i + 1)))
subs.append(("_flameo%d/varcope1." % i, "varcope%02d." % (i + 1)))
subs.append(("_flameo%d/zstat1." % i, "zstat%02d." % (i + 1)))
subs.append(("_flameo%d/tstat1." % i, "tstat%02d." % (i + 1)))
subs.append(("_flameo%d/res4d." % i, "res4d%02d." % (i + 1)))
subs.append(("_warpall%d/cope1_warp." % i, "cope%02d." % (i + 1)))
subs.append(("_warpall%d/varcope1_warp." % (len(conds) + i), "varcope%02d." % (i + 1)))
subs.append(("_warpall%d/zstat1_warp." % (2 * len(conds) + i), "zstat%02d." % (i + 1)))
subs.append(("_warpall%d/cope1_trans." % i, "cope%02d." % (i + 1)))
subs.append(("_warpall%d/varcope1_trans." % (len(conds) + i), "varcope%02d." % (i + 1)))
subs.append(("_warpall%d/zstat1_trans." % (2 * len(conds) + i), "zstat%02d." % (i + 1)))
subs.append(("__get_aparc_means%d/" % i, "/cope%02d_" % (i + 1)))
for i, run_num in enumerate(run_id):
subs.append(("__get_aparc_tsnr%d/" % i, "/run%02d_" % run_num))
subs.append(("__art%d/" % i, "/run%02d_" % run_num))
subs.append(("__dilatemask%d/" % i, "/run%02d_" % run_num))
subs.append(("__realign%d/" % i, "/run%02d_" % run_num))
subs.append(("__modelgen%d/" % i, "/run%02d_" % run_num))
subs.append(("/model%03d/task%03d/" % (model_id, task_id), "/"))
subs.append(("/model%03d/task%03d_" % (model_id, task_id), "/"))
subs.append(("_bold_dtype_mcf_bet_thresh_dil", "_mask"))
subs.append(("_output_warped_image", "_anat2target"))
subs.append(("median_flirt_brain_mask", "median_brain_mask"))
subs.append(("median_bbreg_brain_mask", "median_brain_mask"))
return subs
subsgen = pe.Node(
niu.Function(
input_names=["subject_id", "conds", "run_id", "model_id", "task_id"],
output_names=["substitutions"],
function=get_subs,
),
name="subsgen",
)
wf.connect(subjinfo, "run_id", subsgen, "run_id")
datasink = pe.Node(interface=nio.DataSink(), name="datasink")
wf.connect(infosource, "subject_id", datasink, "container")
wf.connect(infosource, "subject_id", subsgen, "subject_id")
wf.connect(infosource, "model_id", subsgen, "model_id")
wf.connect(infosource, "task_id", subsgen, "task_id")
wf.connect(contrastgen, "contrasts", subsgen, "conds")
wf.connect(subsgen, "substitutions", datasink, "substitutions")
wf.connect(
[
(
fixed_fx.get_node("outputspec"),
datasink,
[
("res4d", "res4d"),
("copes", "copes"),
("varcopes", "varcopes"),
("zstats", "zstats"),
("tstats", "tstats"),
],
)
]
)
wf.connect(
[
(
modelfit.get_node("modelgen"),
datasink,
[
("design_cov", "qa.model"),
("design_image", "qa.model.@matrix_image"),
("design_file", "qa.model.@matrix"),
],
)
]
)
wf.connect(
[
(
preproc,
datasink,
[
("outputspec.motion_parameters", "qa.motion"),
("outputspec.motion_plots", "qa.motion.plots"),
("outputspec.mask", "qa.mask"),
],
)
]
)
wf.connect(registration, "outputspec.mean2anat_mask", datasink, "qa.mask.mean2anat")
wf.connect(art, "norm_files", datasink, "qa.art.@norm")
wf.connect(art, "intensity_files", datasink, "qa.art.@intensity")
wf.connect(art, "outlier_files", datasink, "qa.art.@outlier_files")
wf.connect(registration, "outputspec.anat2target", datasink, "qa.anat2target")
wf.connect(tsnr, "tsnr_file", datasink, "qa.tsnr.@map")
if subjects_dir:
wf.connect(registration, "outputspec.min_cost_file", datasink, "qa.mincost")
wf.connect([(get_roi_tsnr, datasink, [("avgwf_txt_file", "qa.tsnr"), ("summary_file", "qa.tsnr.@summary")])])
wf.connect(
[(get_roi_mean, datasink, [("avgwf_txt_file", "copes.roi"), ("summary_file", "copes.roi.@summary")])]
)
wf.connect(
[(splitfunc, datasink, [("copes", "copes.mni"), ("varcopes", "varcopes.mni"), ("zstats", "zstats.mni")])]
)
wf.connect(calc_median, "median_file", datasink, "mean")
wf.connect(registration, "outputspec.transformed_mean", datasink, "mean.mni")
wf.connect(registration, "outputspec.func2anat_transform", datasink, "xfm.mean2anat")
wf.connect(registration, "outputspec.anat2target_transform", datasink, "xfm.anat2target")
"""
Set processing parameters
"""
preproc.inputs.inputspec.fwhm = fwhm
gethighpass.inputs.hpcutoff = hpcutoff
modelspec.inputs.high_pass_filter_cutoff = hpcutoff
modelfit.inputs.inputspec.bases = {"dgamma": {"derivs": use_derivatives}}
modelfit.inputs.inputspec.model_serial_correlations = True
modelfit.inputs.inputspec.film_threshold = 1000
datasink.inputs.base_directory = output_dir
return wf
def analyze_openfmri_dataset(data_dir, subject=None, model_id=None,
task_id=None, output_dir=None, subj_prefix='*',
hpcutoff=120., use_derivatives=True,
fwhm=6.0, subjects_dir=None, target=None):
"""Analyzes an open fmri dataset
Parameters
----------
data_dir : str
Path to the base data directory
work_dir : str
Nipype working directory (defaults to cwd)
"""
"""
Load nipype workflows
"""
preproc = create_featreg_preproc(whichvol='first')
modelfit = create_modelfit_workflow()
fixed_fx = create_fixed_effects_flow()
if subjects_dir:
registration = create_fs_reg_workflow()
else:
registration = create_reg_workflow()
"""
Remove the plotting connection so that plot iterables don't propagate
to the model stage
"""
preproc.disconnect(preproc.get_node('plot_motion'), 'out_file',
preproc.get_node('outputspec'), 'motion_plots')
"""
Set up openfmri data specific components
"""
subjects = sorted([path.split(os.path.sep)[-1] for path in
glob(os.path.join(data_dir, subj_prefix))])
infosource = pe.Node(niu.IdentityInterface(fields=['subject_id',
'model_id',
'task_id']),
name='infosource')
if len(subject) == 0:
infosource.iterables = [('subject_id', subjects),
('model_id', [model_id]),
('task_id', task_id)]
else:
infosource.iterables = [('subject_id',
[subjects[subjects.index(subj)] for subj in subject]),
('model_id', [model_id]),
('task_id', task_id)]
subjinfo = pe.Node(niu.Function(input_names=['subject_id', 'base_dir',
'task_id', 'model_id'],
output_names=['run_id', 'conds', 'TR'],
function=get_subjectinfo),
name='subjectinfo')
subjinfo.inputs.base_dir = data_dir
"""
Return data components as anat, bold and behav
"""
contrast_file = os.path.join(data_dir, 'models', 'model%03d' % model_id,
'task_contrasts.txt')
has_contrast = os.path.exists(contrast_file)
if has_contrast:
datasource = pe.Node(nio.DataGrabber(infields=['subject_id', 'run_id',
'task_id', 'model_id'],
outfields=['anat', 'bold', 'behav',
'contrasts']),
name='datasource')
else:
datasource = pe.Node(nio.DataGrabber(infields=['subject_id', 'run_id',
'task_id', 'model_id'],
outfields=['anat', 'bold', 'behav']),
name='datasource')
datasource.inputs.base_directory = data_dir
datasource.inputs.template = '*'
if has_contrast:
datasource.inputs.field_template = {'anat': '%s/anatomy/T1_001.nii.gz',
'bold': '%s/BOLD/task%03d_r*/bold.nii.gz',
'behav': ('%s/model/model%03d/onsets/task%03d_'
'run%03d/cond*.txt'),
'contrasts': ('models/model%03d/'
'task_contrasts.txt')}
datasource.inputs.template_args = {'anat': [['subject_id']],
'bold': [['subject_id', 'task_id']],
'behav': [['subject_id', 'model_id',
'task_id', 'run_id']],
'contrasts': [['model_id']]}
else:
datasource.inputs.field_template = {'anat': '%s/anatomy/T1_001.nii.gz',
'bold': '%s/BOLD/task%03d_r*/bold.nii.gz',
'behav': ('%s/model/model%03d/onsets/task%03d_'
'run%03d/cond*.txt')}
datasource.inputs.template_args = {'anat': [['subject_id']],
'bold': [['subject_id', 'task_id']],
'behav': [['subject_id', 'model_id',
'task_id', 'run_id']]}
datasource.inputs.sort_filelist = True
"""
Create meta workflow
"""
wf = pe.Workflow(name='openfmri')
wf.connect(infosource, 'subject_id', subjinfo, 'subject_id')
wf.connect(infosource, 'model_id', subjinfo, 'model_id')
wf.connect(infosource, 'task_id', subjinfo, 'task_id')
wf.connect(infosource, 'subject_id', datasource, 'subject_id')
wf.connect(infosource, 'model_id', datasource, 'model_id')
wf.connect(infosource, 'task_id', datasource, 'task_id')
wf.connect(subjinfo, 'run_id', datasource, 'run_id')
wf.connect([(datasource, preproc, [('bold', 'inputspec.func')]),
])
def get_highpass(TR, hpcutoff):
return hpcutoff / (2 * TR)
gethighpass = pe.Node(niu.Function(input_names=['TR', 'hpcutoff'],
output_names=['highpass'],
function=get_highpass),
name='gethighpass')
wf.connect(subjinfo, 'TR', gethighpass, 'TR')
wf.connect(gethighpass, 'highpass', preproc, 'inputspec.highpass')
"""
Setup a basic set of contrasts, a t-test per condition
"""
def get_contrasts(contrast_file, task_id, conds):
import numpy as np
import os
contrast_def = []
if os.path.exists(contrast_file):
with open(contrast_file, 'rt') as fp:
contrast_def.extend([np.array(row.split()) for row in fp.readlines() if row.strip()])
contrasts = []
for row in contrast_def:
if row[0] != 'task%03d' % task_id:
continue
con = [row[1], 'T', ['cond%03d' % (i + 1) for i in range(len(conds))],
row[2:].astype(float).tolist()]
contrasts.append(con)
# add auto contrasts for each column
for i, cond in enumerate(conds):
con = [cond, 'T', ['cond%03d' % (i + 1)], [1]]
contrasts.append(con)
return contrasts
contrastgen = pe.Node(niu.Function(input_names=['contrast_file',
'task_id', 'conds'],
output_names=['contrasts'],
function=get_contrasts),
name='contrastgen')
art = pe.MapNode(interface=ra.ArtifactDetect(use_differences=[True, False],
use_norm=True,
norm_threshold=1,
zintensity_threshold=3,
parameter_source='FSL',
mask_type='file'),
iterfield=['realigned_files', 'realignment_parameters',
'mask_file'],
name="art")
modelspec = pe.Node(interface=model.SpecifyModel(),
name="modelspec")
modelspec.inputs.input_units = 'secs'
def check_behav_list(behav, run_id, conds):
from nipype.external import six
import numpy as np
num_conds = len(conds)
if isinstance(behav, six.string_types):
behav = [behav]
behav_array = np.array(behav).flatten()
num_elements = behav_array.shape[0]
return behav_array.reshape(num_elements/num_conds, num_conds).tolist()
reshape_behav = pe.Node(niu.Function(input_names=['behav', 'run_id', 'conds'],
output_names=['behav'],
function=check_behav_list),
name='reshape_behav')
wf.connect(subjinfo, 'TR', modelspec, 'time_repetition')
wf.connect(datasource, 'behav', reshape_behav, 'behav')
wf.connect(subjinfo, 'run_id', reshape_behav, 'run_id')
wf.connect(subjinfo, 'conds', reshape_behav, 'conds')
wf.connect(reshape_behav, 'behav', modelspec, 'event_files')
wf.connect(subjinfo, 'TR', modelfit, 'inputspec.interscan_interval')
wf.connect(subjinfo, 'conds', contrastgen, 'conds')
if has_contrast:
wf.connect(datasource, 'contrasts', contrastgen, 'contrast_file')
else:
contrastgen.inputs.contrast_file = ''
wf.connect(infosource, 'task_id', contrastgen, 'task_id')
wf.connect(contrastgen, 'contrasts', modelfit, 'inputspec.contrasts')
wf.connect([(preproc, art, [('outputspec.motion_parameters',
'realignment_parameters'),
('outputspec.realigned_files',
'realigned_files'),
('outputspec.mask', 'mask_file')]),
(preproc, modelspec, [('outputspec.highpassed_files',
'functional_runs'),
('outputspec.motion_parameters',
'realignment_parameters')]),
(art, modelspec, [('outlier_files', 'outlier_files')]),
(modelspec, modelfit, [('session_info',
'inputspec.session_info')]),
(preproc, modelfit, [('outputspec.highpassed_files',
'inputspec.functional_data')])
])
# Comute TSNR on realigned data regressing polynomials upto order 2
tsnr = MapNode(TSNR(regress_poly=2), iterfield=['in_file'], name='tsnr')
wf.connect(preproc, "outputspec.realigned_files", tsnr, "in_file")
# Compute the median image across runs
calc_median = Node(Function(input_names=['in_files'],
output_names=['median_file'],
function=median,
imports=imports),
name='median')
wf.connect(tsnr, 'detrended_file', calc_median, 'in_files')
"""
Reorder the copes so that now it combines across runs
"""
def sort_copes(copes, varcopes, contrasts):
import numpy as np
if not isinstance(copes, list):
copes = [copes]
varcopes = [varcopes]
num_copes = len(contrasts)
n_runs = len(copes)
all_copes = np.array(copes).flatten()
all_varcopes = np.array(varcopes).flatten()
outcopes = all_copes.reshape(len(all_copes)/num_copes, num_copes).T.tolist()
outvarcopes = all_varcopes.reshape(len(all_varcopes)/num_copes, num_copes).T.tolist()
return outcopes, outvarcopes, n_runs
cope_sorter = pe.Node(niu.Function(input_names=['copes', 'varcopes',
'contrasts'],
output_names=['copes', 'varcopes',
'n_runs'],
function=sort_copes),
name='cope_sorter')
pickfirst = lambda x: x[0]
wf.connect(contrastgen, 'contrasts', cope_sorter, 'contrasts')
wf.connect([(preproc, fixed_fx, [(('outputspec.mask', pickfirst),
'flameo.mask_file')]),
(modelfit, cope_sorter, [('outputspec.copes', 'copes')]),
(modelfit, cope_sorter, [('outputspec.varcopes', 'varcopes')]),
(cope_sorter, fixed_fx, [('copes', 'inputspec.copes'),
('varcopes', 'inputspec.varcopes'),
('n_runs', 'l2model.num_copes')]),
(modelfit, fixed_fx, [('outputspec.dof_file',
'inputspec.dof_files'),
])
])
wf.connect(calc_median, 'median_file', registration, 'inputspec.mean_image')
if subjects_dir:
wf.connect(infosource, 'subject_id', registration, 'inputspec.subject_id')
registration.inputs.inputspec.subjects_dir = subjects_dir
registration.inputs.inputspec.target_image = fsl.Info.standard_image('MNI152_T1_2mm_brain.nii.gz')
if target:
registration.inputs.inputspec.target_image = target
else:
wf.connect(datasource, 'anat', registration, 'inputspec.anatomical_image')
registration.inputs.inputspec.target_image = fsl.Info.standard_image('MNI152_T1_2mm.nii.gz')
registration.inputs.inputspec.target_image_brain = fsl.Info.standard_image('MNI152_T1_2mm_brain.nii.gz')
registration.inputs.inputspec.config_file = 'T1_2_MNI152_2mm'
def merge_files(copes, varcopes, zstats):
out_files = []
splits = []
out_files.extend(copes)
splits.append(len(copes))
out_files.extend(varcopes)
splits.append(len(varcopes))
out_files.extend(zstats)
splits.append(len(zstats))
return out_files, splits
mergefunc = pe.Node(niu.Function(input_names=['copes', 'varcopes',
'zstats'],
output_names=['out_files', 'splits'],
function=merge_files),
name='merge_files')
wf.connect([(fixed_fx.get_node('outputspec'), mergefunc,
[('copes', 'copes'),
('varcopes', 'varcopes'),
('zstats', 'zstats'),
])])
wf.connect(mergefunc, 'out_files', registration, 'inputspec.source_files')
def split_files(in_files, splits):
copes = in_files[:splits[0]]
varcopes = in_files[splits[0]:(splits[0] + splits[1])]
zstats = in_files[(splits[0] + splits[1]):]
return copes, varcopes, zstats
splitfunc = pe.Node(niu.Function(input_names=['in_files', 'splits'],
output_names=['copes', 'varcopes',
'zstats'],
function=split_files),
name='split_files')
wf.connect(mergefunc, 'splits', splitfunc, 'splits')
wf.connect(registration, 'outputspec.transformed_files',
splitfunc, 'in_files')
if subjects_dir:
get_roi_mean = pe.MapNode(fs.SegStats(default_color_table=True),
iterfield=['in_file'], name='get_aparc_means')
get_roi_mean.inputs.avgwf_txt_file = True
wf.connect(fixed_fx.get_node('outputspec'), 'copes', get_roi_mean, 'in_file')
wf.connect(registration, 'outputspec.aparc', get_roi_mean, 'segmentation_file')
get_roi_tsnr = pe.MapNode(fs.SegStats(default_color_table=True),
iterfield=['in_file'], name='get_aparc_tsnr')
get_roi_tsnr.inputs.avgwf_txt_file = True
wf.connect(tsnr, 'tsnr_file', get_roi_tsnr, 'in_file')
wf.connect(registration, 'outputspec.aparc', get_roi_tsnr, 'segmentation_file')
"""
Connect to a datasink
"""
def get_subs(subject_id, conds, run_id, model_id, task_id):
subs = [('_subject_id_%s_' % subject_id, '')]
subs.append(('_model_id_%d' % model_id, 'model%03d' %model_id))
subs.append(('task_id_%d/' % task_id, '/task%03d_' % task_id))
subs.append(('bold_dtype_mcf_mask_smooth_mask_gms_tempfilt_mean_warp',
'mean'))
subs.append(('bold_dtype_mcf_mask_smooth_mask_gms_tempfilt_mean_flirt',
'affine'))
for i in range(len(conds)):
subs.append(('_flameo%d/cope1.' % i, 'cope%02d.' % (i + 1)))
subs.append(('_flameo%d/varcope1.' % i, 'varcope%02d.' % (i + 1)))
subs.append(('_flameo%d/zstat1.' % i, 'zstat%02d.' % (i + 1)))
subs.append(('_flameo%d/tstat1.' % i, 'tstat%02d.' % (i + 1)))
subs.append(('_flameo%d/res4d.' % i, 'res4d%02d.' % (i + 1)))
subs.append(('_warpall%d/cope1_warp.' % i,
'cope%02d.' % (i + 1)))
subs.append(('_warpall%d/varcope1_warp.' % (len(conds) + i),
'varcope%02d.' % (i + 1)))
subs.append(('_warpall%d/zstat1_warp.' % (2 * len(conds) + i),
'zstat%02d.' % (i + 1)))
subs.append(('_warpall%d/cope1_trans.' % i,
'cope%02d.' % (i + 1)))
subs.append(('_warpall%d/varcope1_trans.' % (len(conds) + i),
'varcope%02d.' % (i + 1)))
subs.append(('_warpall%d/zstat1_trans.' % (2 * len(conds) + i),
'zstat%02d.' % (i + 1)))
subs.append(('__get_aparc_means%d/' % i, '/cope%02d_' % (i + 1)))
for i, run_num in enumerate(run_id):
subs.append(('__get_aparc_tsnr%d/' % i, '/run%02d_' % run_num))
subs.append(('__art%d/' % i, '/run%02d_' % run_num))
subs.append(('__dilatemask%d/' % i, '/run%02d_' % run_num))
subs.append(('__realign%d/' % i, '/run%02d_' % run_num))
subs.append(('__modelgen%d/' % i, '/run%02d_' % run_num))
subs.append(('/model%03d/task%03d/' % (model_id, task_id), '/'))
subs.append(('/model%03d/task%03d_' % (model_id, task_id), '/'))
subs.append(('_bold_dtype_mcf_bet_thresh_dil', '_mask'))
subs.append(('_output_warped_image', '_anat2target'))
subs.append(('median_flirt_brain_mask', 'median_brain_mask'))
subs.append(('median_bbreg_brain_mask', 'median_brain_mask'))
return subs
subsgen = pe.Node(niu.Function(input_names=['subject_id', 'conds', 'run_id',
'model_id', 'task_id'],
output_names=['substitutions'],
function=get_subs),
name='subsgen')
wf.connect(subjinfo, 'run_id', subsgen, 'run_id')
datasink = pe.Node(interface=nio.DataSink(),
name="datasink")
wf.connect(infosource, 'subject_id', datasink, 'container')
wf.connect(infosource, 'subject_id', subsgen, 'subject_id')
wf.connect(infosource, 'model_id', subsgen, 'model_id')
wf.connect(infosource, 'task_id', subsgen, 'task_id')
wf.connect(contrastgen, 'contrasts', subsgen, 'conds')
wf.connect(subsgen, 'substitutions', datasink, 'substitutions')
wf.connect([(fixed_fx.get_node('outputspec'), datasink,
[('res4d', 'res4d'),
('copes', 'copes'),
('varcopes', 'varcopes'),
('zstats', 'zstats'),
('tstats', 'tstats')])
])
wf.connect([(modelfit.get_node('modelgen'), datasink,
[('design_cov', 'qa.model'),
('design_image', 'qa.model.@matrix_image'),
('design_file', 'qa.model.@matrix'),
])])
wf.connect([(preproc, datasink, [('outputspec.motion_parameters',
'qa.motion'),
('outputspec.motion_plots',
'qa.motion.plots'),
('outputspec.mask', 'qa.mask')])])
wf.connect(registration, 'outputspec.mean2anat_mask', datasink, 'qa.mask.mean2anat')
wf.connect(art, 'norm_files', datasink, 'qa.art.@norm')
wf.connect(art, 'intensity_files', datasink, 'qa.art.@intensity')
wf.connect(art, 'outlier_files', datasink, 'qa.art.@outlier_files')
wf.connect(registration, 'outputspec.anat2target', datasink, 'qa.anat2target')
wf.connect(tsnr, 'tsnr_file', datasink, 'qa.tsnr.@map')
if subjects_dir:
wf.connect(registration, 'outputspec.min_cost_file', datasink, 'qa.mincost')
wf.connect([(get_roi_tsnr, datasink, [('avgwf_txt_file', 'qa.tsnr'),
('summary_file', 'qa.tsnr.@summary')])])
wf.connect([(get_roi_mean, datasink, [('avgwf_txt_file', 'copes.roi'),
('summary_file', 'copes.roi.@summary')])])
wf.connect([(splitfunc, datasink,
[('copes', 'copes.mni'),
('varcopes', 'varcopes.mni'),
('zstats', 'zstats.mni'),
])])
wf.connect(calc_median, 'median_file', datasink, 'mean')
wf.connect(registration, 'outputspec.transformed_mean', datasink, 'mean.mni')
wf.connect(registration, 'outputspec.func2anat_transform', datasink, 'xfm.mean2anat')
wf.connect(registration, 'outputspec.anat2target_transform', datasink, 'xfm.anat2target')
"""
Set processing parameters
"""
preproc.inputs.inputspec.fwhm = fwhm
gethighpass.inputs.hpcutoff = hpcutoff
modelspec.inputs.high_pass_filter_cutoff = hpcutoff
modelfit.inputs.inputspec.bases = {'dgamma': {'derivs': use_derivatives}}
modelfit.inputs.inputspec.model_serial_correlations = True
modelfit.inputs.inputspec.film_threshold = 1000
datasink.inputs.base_directory = output_dir
return wf
def create_workflow(contrasts, combine_runs=True):
level1_workflow = pe.Workflow(name='level1flow')
# ===================================================================
# _____ _
# |_ _| | |
# | | _ __ _ __ _ _| |_
# | | | '_ \| '_ \| | | | __|
# _| |_| | | | |_) | |_| | |_
# |_____|_| |_| .__/ \__,_|\__|
# | |
# |_|
# ===================================================================
# ------------------ Specify variables
inputnode = pe.Node(
niu.IdentityInterface(fields=[
#'funcmasks',
'fwhm', # smoothing
'highpass',
'funcs',
'event_log',
'motion_parameters',
'motion_outlier_files',
'ref_func',
'ref_funcmask',
]),
name="inputspec")
def remove_runs_missing_funcs(in_files, in_funcs):
import os
# import pdb
import re
# if input.synchronize = True, then in_files and in_funcs will
# be single strings
assert not isinstance(in_files, str), "in_files must be list"
assert not isinstance(in_funcs, str), "in_funcs must be list"
if isinstance(in_files, str):
in_files = [in_files]
if isinstance(in_funcs, str):
in_funcs = [in_funcs]
has_func = set()
for f in in_funcs:
base = os.path.basename(f)
try:
sub = re.search(r'sub-([a-zA-Z0-9]+)_', base).group(1)
ses = re.search(r'ses-([a-zA-Z0-9]+)_', base).group(1)
run = re.search(r'run-([a-zA-Z0-9]+)_', base).group(1)
except AttributeError as e:
raise RuntimeError(
'Could not process "sub-*_", "ses-*_", or "run-*_" from func "%s"'
% f)
has_func.add((sub, ses, run))
files = []
for f in in_files:
base = os.path.basename(f)
try:
sub = re.search(r'sub-([a-zA-Z0-9]+)_', base).group(1)
ses = re.search(r'ses-([a-zA-Z0-9]+)_', base).group(1)
run = re.search(r'run-([a-zA-Z0-9]+)_', base).group(1)
except AttributeError as e:
raise RuntimeError(
'Could not process "sub-*_", "ses-*_", or "run-*_" from event file "%s"'
% f)
if (sub, ses, run) in has_func:
files.append(f)
return files
input_events = pe.Node(
interface=niu.Function(input_names=['in_files', 'in_funcs'],
output_names=['out_files'],
function=remove_runs_missing_funcs),
name='input_events',
)
level1_workflow.connect([
(inputnode, input_events, [
('funcs', 'in_funcs'),
('event_log', 'in_files'),
]),
])
# -------------------------------------------------------------------
# /~_ _ _ _ _. _ _ . _ _ |. _ _
# \_/(/_| |(/_| |(_ |_)||_)(/_||| |(/_
# | |
# -------------------------------------------------------------------
"""
Preliminaries
-------------
Setup any package specific configuration. The output file format for FSL
routines is being set to compressed NIFTI.
"""
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
modelfit = fslflows.create_modelfit_workflow()
if combine_runs:
fixed_fx = fslflows.create_fixed_effects_flow()
else:
fixed_fx = None
"""
Artifact detection is done in preprocessing workflow.
"""
"""
Add model specification nodes between the preprocessing and modelfitting
workflows.
"""
modelspec = pe.Node(model.SpecifyModel(), name="modelspec")
"""
Set up first-level workflow
---------------------------
"""
def sort_copes(files):
""" Sort by copes and the runs, ie.
[[cope1_run1, cope1_run2], [cope2_run1, cope2_run2]]
"""
assert files[0] is not str
numcopes = len(files[0])
assert numcopes > 1
outfiles = []
for i in range(numcopes):
outfiles.insert(i, [])
for j, elements in enumerate(files):
outfiles[i].append(elements[i])
return outfiles
def num_copes(files):
return len(files)
if fixed_fx is not None:
level1_workflow.connect([
(inputnode, fixed_fx, [('ref_funcmask', 'flameo.mask_file')
]), # To-do: use reference mask!!!
(modelfit, fixed_fx, [
(('outputspec.copes', sort_copes), 'inputspec.copes'),
('outputspec.dof_file', 'inputspec.dof_files'),
(('outputspec.varcopes', sort_copes), 'inputspec.varcopes'),
(('outputspec.copes', num_copes), 'l2model.num_copes'),
])
])
# -------------------------------------------------------------------
# /~\ _|_ _ _|_
# \_/|_|| |_)|_||
# |
# -------------------------------------------------------------------
# Datasink
outputfiles = pe.Node(nio.DataSink(base_directory=ds_root,
container='derivatives/modelfit',
parameterization=True),
name="output_files")
# Use the following DataSink output substitutions
outputfiles.inputs.substitutions = [
('subject_id_', 'sub-'),
('session_id_', 'ses-'),
# ('/mask/', '/'),
# ('_preproc_flirt_thresh.nii.gz', '_transformedmask.nii.gz'),
# ('_preproc_volreg_unwarped.nii.gz', '_preproc.nii.gz'),
# ('_preproc_flirt_unwarped.nii.gz', '_preproc-mask.nii.gz'),
# ('/_mc_method_afni3dvolreg/', '/'),
# ('/funcs/', '/'),
# ('/funcmasks/', '/'),
# ('preproc_volreg.nii.gz', 'preproc.nii.gz'),
('/_mc_method_afni3dAllinSlices/', '/'),
]
# Put result into a BIDS-like format
outputfiles.inputs.regexp_substitutions = [
(r'_ses-([a-zA-Z0-9]+)_sub-([a-zA-Z0-9]+)', r'sub-\2/ses-\1'),
# (r'/_addmean[0-9]+/', r'/func/'),
# (r'/_dilatemask[0-9]+/', r'/func/'),
# (r'/_funcbrain[0-9]+/', r'/func/'),
# (r'/_maskfunc[0-9]+/', r'/func/'),
# (r'/_mc[0-9]+/', r'/func/'),
# (r'/_meanfunc[0-9]+/', r'/func/'),
# (r'/_outliers[0-9]+/', r'/func/'),
# (r'/_undistort_masks[0-9]+/', r'/func/'),
# (r'/_undistort[0-9]+/', r'/func/'),
]
level1_workflow.connect([
(modelfit, outputfiles, [
(('outputspec.copes', sort_copes), 'copes'),
('outputspec.dof_file', 'dof_files'),
(('outputspec.varcopes', sort_copes), 'varcopes'),
]),
])
if fixed_fx is not None:
level1_workflow.connect([
(fixed_fx, outputfiles, [
('outputspec.res4d', 'fx.res4d'),
('outputspec.copes', 'fx.copes'),
('outputspec.varcopes', 'fx.varcopes'),
('outputspec.zstats', 'fx.zstats'),
('outputspec.tstats', 'fx.tstats'),
]),
])
# -------------------------------------------------------------------
# (~ _ _ _. _ _ _ _ _|_ _ _ _ _. |`. _
# (_><|_)(/_| || | |(/_| | | _\|_)(/_(_|~|~|(_
# | |
# -------------------------------------------------------------------
# """
# Experiment specific components
# ------------------------------
# """
"""
Use the get_node function to retrieve an internal node by name. Then set the
iterables on this node to perform two different extents of smoothing.
"""
featinput = level1_workflow.get_node('modelfit.inputspec')
# featinput.iterables = ('fwhm', [5., 10.])
featinput.inputs.fwhm = 2.0
hpcutoff_s = 50. # FWHM in seconds
TR = 2.5
hpcutoff_nvol = hpcutoff_s / 2.5 # FWHM in volumns
# Use Python3 for processing. See code/requirements.txt for pip packages.
featinput.inputs.highpass = hpcutoff_nvol / 2.355 # Gaussian: σ in volumes - (REMEMBER to run with Python 3)
"""
Setup a function that returns subject-specific information about the
experimental paradigm. This is used by the
:class:`nipype.modelgen.SpecifyModel` to create the information necessary
to generate an SPM design matrix. In this tutorial, the same paradigm was used
for every participant. Other examples of this function are available in the
`doc/examples` folder. Note: Python knowledge required here.
"""
# from timeevents.curvetracing import calc_curvetracing_events
from timeevents import process_time_events
timeevents = pe.MapNode(
interface=process_time_events, # calc_curvetracing_events,
iterfield=('event_log', 'in_nvols', 'TR'),
name='timeevents')
def get_nvols(funcs):
import nibabel as nib
nvols = []
if isinstance(funcs, str):
funcs = [funcs]
for func in funcs:
func_img = nib.load(func)
header = func_img.header
try:
nvols.append(func_img.get_data().shape[3])
except IndexError as e:
# if shape only has 3 dimensions, then it is only 1 volume
nvols.append(1)
return (nvols)
def get_TR(funcs):
import nibabel as nib
TRs = []
if isinstance(funcs, str):
funcs = [funcs]
for func in funcs:
func_img = nib.load(func)
header = func_img.header
try:
TR = round(header.get_zooms()[3], 5)
except IndexError as e:
TR = 2.5
print("Warning: %s did not have TR defined in the header. "
"Using default TR of %0.2f" % (func, TR))
assert TR > 1
TRs.append(TR)
return (TRs)
level1_workflow.connect([
(inputnode, timeevents, [
(('funcs', get_nvols), 'in_nvols'),
(('funcs', get_TR), 'TR'),
]),
(input_events, timeevents, [('out_files', 'event_log')]),
(inputnode, modelspec, [('motion_parameters', 'realignment_parameters')
]),
(modelspec, modelfit, [('session_info', 'inputspec.session_info')]),
])
# Ignore volumes after last good response
filter_outliers = pe.MapNode(interface=FilterNumsTask(),
name='filter_outliers',
iterfield=('in_file', 'max_number'))
level1_workflow.connect([
(inputnode, filter_outliers, [('motion_outlier_files', 'in_file')]),
(filter_outliers, modelspec, [('out_file', 'outlier_files')]),
(timeevents, filter_outliers, [('out_nvols', 'max_number')]),
])
def evt_info(cond_events):
output = []
# for each run
for ev in cond_events:
from nipype.interfaces.base import Bunch
from copy import deepcopy
names = []
for name in ev.keys():
if ev[name].shape[0] > 0:
names.append(name)
onsets = [
deepcopy(ev[name].time) if ev[name].shape[0] > 0 else []
for name in names
]
durations = [
deepcopy(ev[name].dur) if ev[name].shape[0] > 0 else []
for name in names
]
amplitudes = [
deepcopy(ev[name].amplitude) if ev[name].shape[0] > 0 else []
for name in names
]
run_results = Bunch(
conditions=names,
onsets=[deepcopy(ev[name].time) for name in names],
durations=[deepcopy(ev[name].dur) for name in names],
amplitudes=[deepcopy(ev[name].amplitude) for name in names])
output.append(run_results)
return output
modelspec.inputs.input_units = 'secs'
modelspec.inputs.time_repetition = TR # to-do: specify per func
modelspec.inputs.high_pass_filter_cutoff = hpcutoff_s
modelfit.inputs.inputspec.interscan_interval = TR # to-do: specify per func
modelfit.inputs.inputspec.bases = {'dgamma': {'derivs': True}}
modelfit.inputs.inputspec.contrasts = contrasts
modelfit.inputs.inputspec.model_serial_correlations = True
modelfit.inputs.inputspec.film_threshold = 1000
# level1_workflow.base_dir = os.path.abspath('./workingdirs/level1flow')
modelfit.config['execution'] = dict(crashdump_dir=os.path.abspath('.'))
# Ignore volumes after subject has finished working for the run
beh_roi = pe.MapNode(fsl.ExtractROI(t_min=0),
name='beh_roi',
iterfield=['in_file', 't_size'])
level1_workflow.connect([
(timeevents, modelspec, [
(('out_events', evt_info), 'subject_info'),
]),
(inputnode, beh_roi, [
('funcs', 'in_file'),
]),
(timeevents, beh_roi, [
('out_nvols', 't_size'),
]),
(beh_roi, modelspec, [
('roi_file', 'functional_runs'),
]),
(beh_roi, modelfit, [
('roi_file', 'inputspec.functional_data'),
]),
(beh_roi, outputfiles, [
('roi_file', 'roi_file'),
]),
# (inputnode, datasource, [('in_data', 'base_directory')]),
# (infosource, datasource, [('subject_id', 'subject_id')]),
# (infosource, modelspec, [(('subject_id', subjectinfo), 'subject_info')]),
# (datasource, preproc, [('func', 'inputspec.func')]),
])
return (level1_workflow)
def analyze_openfmri_dataset(data_dir, subject=None, model_id=None,
task_id=None, output_dir=None):
"""Analyzes an open fmri dataset
Parameters
----------
data_dir : str
Path to the base data directory
work_dir : str
Nipype working directory (defaults to cwd)
"""
"""
Load nipype workflows
"""
preproc = create_featreg_preproc(whichvol='first')
modelfit = create_modelfit_workflow()
fixed_fx = create_fixed_effects_flow()
registration = create_reg_workflow()
"""
Remove the plotting connection so that plot iterables don't propagate
to the model stage
"""
preproc.disconnect(preproc.get_node('plot_motion'), 'out_file',
preproc.get_node('outputspec'), 'motion_plots')
"""
Set up openfmri data specific components
"""
subjects = sorted([path.split(os.path.sep)[-1] for path in
glob(os.path.join(data_dir, 'sub*'))])
infosource = pe.Node(niu.IdentityInterface(fields=['subject_id',
'model_id',
'task_id']),
name='infosource')
if subject is None:
infosource.iterables = [('subject_id', subjects),
('model_id', [model_id]),
('task_id', [task_id])]
else:
infosource.iterables = [('subject_id',
[subjects[subjects.index(subject)]]),
('model_id', [model_id]),
('task_id', [task_id])]
subjinfo = pe.Node(niu.Function(input_names=['subject_id', 'base_dir',
'task_id', 'model_id'],
output_names=['run_id', 'conds', 'TR'],
function=get_subjectinfo),
name='subjectinfo')
subjinfo.inputs.base_dir = data_dir
"""
Return data components as anat, bold and behav
"""
datasource = pe.Node(nio.DataGrabber(infields=['subject_id', 'run_id',
'task_id', 'model_id'],
outfields=['anat', 'bold', 'behav',
'contrasts']),
name='datasource')
datasource.inputs.base_directory = data_dir
datasource.inputs.template = '*'
datasource.inputs.field_template = {'anat': '%s/anatomy/highres001.nii.gz',
'bold': '%s/BOLD/task%03d_r*/bold.nii.gz',
'behav': ('%s/model/model%03d/onsets/task%03d_'
'run%03d/cond*.txt'),
'contrasts': ('models/model%03d/'
'task_contrasts.txt')}
datasource.inputs.template_args = {'anat': [['subject_id']],
'bold': [['subject_id', 'task_id']],
'behav': [['subject_id', 'model_id',
'task_id', 'run_id']],
'contrasts': [['model_id']]}
datasource.inputs.sort_filelist = True
"""
Create meta workflow
"""
wf = pe.Workflow(name='openfmri')
wf.connect(infosource, 'subject_id', subjinfo, 'subject_id')
wf.connect(infosource, 'model_id', subjinfo, 'model_id')
wf.connect(infosource, 'task_id', subjinfo, 'task_id')
wf.connect(infosource, 'subject_id', datasource, 'subject_id')
wf.connect(infosource, 'model_id', datasource, 'model_id')
wf.connect(infosource, 'task_id', datasource, 'task_id')
wf.connect(subjinfo, 'run_id', datasource, 'run_id')
wf.connect([(datasource, preproc, [('bold', 'inputspec.func')]),
])
def get_highpass(TR, hpcutoff):
return hpcutoff / (2 * TR)
gethighpass = pe.Node(niu.Function(input_names=['TR', 'hpcutoff'],
output_names=['highpass'],
function=get_highpass),
name='gethighpass')
wf.connect(subjinfo, 'TR', gethighpass, 'TR')
wf.connect(gethighpass, 'highpass', preproc, 'inputspec.highpass')
"""
Setup a basic set of contrasts, a t-test per condition
"""
def get_contrasts(contrast_file, task_id, conds):
import numpy as np
contrast_def = np.genfromtxt(contrast_file, dtype=object)
if len(contrast_def.shape) == 1:
contrast_def = contrast_def[None, :]
contrasts = []
for row in contrast_def:
if row[0] != 'task%03d' % task_id:
continue
con = [row[1], 'T', ['cond%03d' % (i + 1) for i in range(len(conds))],
row[2:].astype(float).tolist()]
contrasts.append(con)
# add auto contrasts for each column
for i, cond in enumerate(conds):
con = [cond, 'T', ['cond%03d' % (i + 1)], [1]]
contrasts.append(con)
return contrasts
contrastgen = pe.Node(niu.Function(input_names=['contrast_file',
'task_id', 'conds'],
output_names=['contrasts'],
function=get_contrasts),
name='contrastgen')
art = pe.MapNode(interface=ra.ArtifactDetect(use_differences=[True, False],
use_norm=True,
norm_threshold=1,
zintensity_threshold=3,
parameter_source='FSL',
mask_type='file'),
iterfield=['realigned_files', 'realignment_parameters',
'mask_file'],
name="art")
modelspec = pe.Node(interface=model.SpecifyModel(),
name="modelspec")
modelspec.inputs.input_units = 'secs'
wf.connect(subjinfo, 'TR', modelspec, 'time_repetition')
wf.connect(datasource, 'behav', modelspec, 'event_files')
wf.connect(subjinfo, 'TR', modelfit, 'inputspec.interscan_interval')
wf.connect(subjinfo, 'conds', contrastgen, 'conds')
wf.connect(datasource, 'contrasts', contrastgen, 'contrast_file')
wf.connect(infosource, 'task_id', contrastgen, 'task_id')
wf.connect(contrastgen, 'contrasts', modelfit, 'inputspec.contrasts')
wf.connect([(preproc, art, [('outputspec.motion_parameters',
'realignment_parameters'),
('outputspec.realigned_files',
'realigned_files'),
('outputspec.mask', 'mask_file')]),
(preproc, modelspec, [('outputspec.highpassed_files',
'functional_runs'),
('outputspec.motion_parameters',
'realignment_parameters')]),
(art, modelspec, [('outlier_files', 'outlier_files')]),
(modelspec, modelfit, [('session_info',
'inputspec.session_info')]),
(preproc, modelfit, [('outputspec.highpassed_files',
'inputspec.functional_data')])
])
"""
Reorder the copes so that now it combines across runs
"""
def sort_copes(files):
numelements = len(files[0])
outfiles = []
for i in range(numelements):
outfiles.insert(i, [])
for j, elements in enumerate(files):
outfiles[i].append(elements[i])
return outfiles
def num_copes(files):
return len(files)
pickfirst = lambda x: x[0]
wf.connect([(preproc, fixed_fx, [(('outputspec.mask', pickfirst),
'flameo.mask_file')]),
(modelfit, fixed_fx, [(('outputspec.copes', sort_copes),
'inputspec.copes'),
('outputspec.dof_file',
'inputspec.dof_files'),
(('outputspec.varcopes',
sort_copes),
'inputspec.varcopes'),
(('outputspec.copes', num_copes),
'l2model.num_copes'),
])
])
wf.connect(preproc, 'outputspec.mean', registration, 'inputspec.mean_image')
wf.connect(datasource, 'anat', registration, 'inputspec.anatomical_image')
registration.inputs.inputspec.target_image = fsl.Info.standard_image('MNI152_T1_2mm.nii.gz')
def merge_files(copes, varcopes):
out_files = []
splits = []
out_files.extend(copes)
splits.append(len(copes))
out_files.extend(varcopes)
splits.append(len(varcopes))
return out_files, splits
mergefunc = pe.Node(niu.Function(input_names=['copes', 'varcopes'],
output_names=['out_files', 'splits'],
function=merge_files),
name='merge_files')
wf.connect([(fixed_fx.get_node('outputspec'), mergefunc,
[('copes', 'copes'),
('varcopes', 'varcopes'),
])])
wf.connect(mergefunc, 'out_files', registration, 'inputspec.source_files')
def split_files(in_files, splits):
copes = in_files[:splits[1]]
varcopes = in_files[splits[1]:]
return copes, varcopes
splitfunc = pe.Node(niu.Function(input_names=['in_files', 'splits'],
output_names=['copes', 'varcopes'],
function=split_files),
name='split_files')
wf.connect(mergefunc, 'splits', splitfunc, 'splits')
wf.connect(registration, 'outputspec.transformed_files',
splitfunc, 'in_files')
"""
Connect to a datasink
"""
def get_subs(subject_id, conds, model_id, task_id):
subs = [('_subject_id_%s_' % subject_id, '')]
subs.append(('_model_id_%d' % model_id, 'model%03d' %model_id))
subs.append(('task_id_%d/' % task_id, '/task%03d_' % task_id))
subs.append(('bold_dtype_mcf_mask_smooth_mask_gms_tempfilt_mean_warp_warp',
'mean'))
for i in range(len(conds)):
subs.append(('_flameo%d/cope1.' % i, 'cope%02d.' % (i + 1)))
subs.append(('_flameo%d/varcope1.' % i, 'varcope%02d.' % (i + 1)))
subs.append(('_flameo%d/zstat1.' % i, 'zstat%02d.' % (i + 1)))
subs.append(('_flameo%d/tstat1.' % i, 'tstat%02d.' % (i + 1)))
subs.append(('_flameo%d/res4d.' % i, 'res4d%02d.' % (i + 1)))
subs.append(('_warpall%d/cope1_warp_warp.' % i,
'cope%02d.' % (i + 1)))
subs.append(('_warpall%d/varcope1_warp_warp.' % (len(conds) + i),
'varcope%02d.' % (i + 1)))
return subs
subsgen = pe.Node(niu.Function(input_names=['subject_id', 'conds',
'model_id', 'task_id'],
output_names=['substitutions'],
function=get_subs),
name='subsgen')
datasink = pe.Node(interface=nio.DataSink(),
name="datasink")
wf.connect(infosource, 'subject_id', datasink, 'container')
wf.connect(infosource, 'subject_id', subsgen, 'subject_id')
wf.connect(infosource, 'model_id', subsgen, 'model_id')
wf.connect(infosource, 'task_id', subsgen, 'task_id')
wf.connect(contrastgen, 'contrasts', subsgen, 'conds')
wf.connect(subsgen, 'substitutions', datasink, 'substitutions')
wf.connect([(fixed_fx.get_node('outputspec'), datasink,
[('res4d', 'res4d'),
('copes', 'copes'),
('varcopes', 'varcopes'),
('zstats', 'zstats'),
('tstats', 'tstats')])
])
wf.connect([(splitfunc, datasink,
[('copes', 'copes.mni'),
('varcopes', 'varcopes.mni'),
])])
wf.connect(registration, 'outputspec.transformed_mean', datasink, 'mean.mni')
"""
Set processing parameters
"""
hpcutoff = 120.
preproc.inputs.inputspec.fwhm = 6.0
gethighpass.inputs.hpcutoff = hpcutoff
modelspec.inputs.high_pass_filter_cutoff = hpcutoff
modelfit.inputs.inputspec.bases = {'dgamma': {'derivs': True}}
modelfit.inputs.inputspec.model_serial_correlations = True
modelfit.inputs.inputspec.film_threshold = 1000
datasink.inputs.base_directory = output_dir
return wf
def analyze_openfmri_dataset(data_dir,
subject=None,
model_id=None,
task_id=None,
output_dir=None,
subj_prefix='*',
hpcutoff=120.,
use_derivatives=True,
fwhm=6.0,
subjects_dir=None,
target=None):
"""Analyzes an open fmri dataset
Parameters
----------
data_dir : str
Path to the base data directory
work_dir : str
Nipype working directory (defaults to cwd)
"""
"""
Load nipype workflows
"""
preproc = create_featreg_preproc(whichvol='first')
modelfit = create_modelfit_workflow()
fixed_fx = create_fixed_effects_flow()
if subjects_dir:
registration = create_fs_reg_workflow()
else:
registration = create_reg_workflow()
"""
Remove the plotting connection so that plot iterables don't propagate
to the model stage
"""
preproc.disconnect(
preproc.get_node('plot_motion'), 'out_file',
preproc.get_node('outputspec'), 'motion_plots')
"""
Set up openfmri data specific components
"""
subjects = sorted([
path.split(os.path.sep)[-1]
for path in glob(os.path.join(data_dir, subj_prefix))
])
infosource = pe.Node(
niu.IdentityInterface(fields=['subject_id', 'model_id', 'task_id']),
name='infosource')
if len(subject) == 0:
infosource.iterables = [('subject_id', subjects),
('model_id', [model_id]), ('task_id', task_id)]
else:
infosource.iterables = [('subject_id', [
subjects[subjects.index(subj)] for subj in subject
]), ('model_id', [model_id]), ('task_id', task_id)]
subjinfo = pe.Node(
niu.Function(
input_names=['subject_id', 'base_dir', 'task_id', 'model_id'],
output_names=['run_id', 'conds', 'TR'],
function=get_subjectinfo),
name='subjectinfo')
subjinfo.inputs.base_dir = data_dir
"""
Return data components as anat, bold and behav
"""
contrast_file = os.path.join(data_dir, 'models', 'model%03d' % model_id,
'task_contrasts.txt')
has_contrast = os.path.exists(contrast_file)
if has_contrast:
datasource = pe.Node(
nio.DataGrabber(
infields=['subject_id', 'run_id', 'task_id', 'model_id'],
outfields=['anat', 'bold', 'behav', 'contrasts']),
name='datasource')
else:
datasource = pe.Node(
nio.DataGrabber(
infields=['subject_id', 'run_id', 'task_id', 'model_id'],
outfields=['anat', 'bold', 'behav']),
name='datasource')
datasource.inputs.base_directory = data_dir
datasource.inputs.template = '*'
if has_contrast:
datasource.inputs.field_template = {
'anat': '%s/anatomy/T1_001.nii.gz',
'bold': '%s/BOLD/task%03d_r*/bold.nii.gz',
'behav': ('%s/model/model%03d/onsets/task%03d_'
'run%03d/cond*.txt'),
'contrasts': ('models/model%03d/'
'task_contrasts.txt')
}
datasource.inputs.template_args = {
'anat': [['subject_id']],
'bold': [['subject_id', 'task_id']],
'behav': [['subject_id', 'model_id', 'task_id', 'run_id']],
'contrasts': [['model_id']]
}
else:
datasource.inputs.field_template = {
'anat': '%s/anatomy/T1_001.nii.gz',
'bold': '%s/BOLD/task%03d_r*/bold.nii.gz',
'behav': ('%s/model/model%03d/onsets/task%03d_'
'run%03d/cond*.txt')
}
datasource.inputs.template_args = {
'anat': [['subject_id']],
'bold': [['subject_id', 'task_id']],
'behav': [['subject_id', 'model_id', 'task_id', 'run_id']]
}
datasource.inputs.sort_filelist = True
"""
Create meta workflow
"""
wf = pe.Workflow(name='openfmri')
wf.connect(infosource, 'subject_id', subjinfo, 'subject_id')
wf.connect(infosource, 'model_id', subjinfo, 'model_id')
wf.connect(infosource, 'task_id', subjinfo, 'task_id')
wf.connect(infosource, 'subject_id', datasource, 'subject_id')
wf.connect(infosource, 'model_id', datasource, 'model_id')
wf.connect(infosource, 'task_id', datasource, 'task_id')
wf.connect(subjinfo, 'run_id', datasource, 'run_id')
wf.connect([
(datasource, preproc, [('bold', 'inputspec.func')]),
])
def get_highpass(TR, hpcutoff):
return hpcutoff / (2. * TR)
gethighpass = pe.Node(
niu.Function(
input_names=['TR', 'hpcutoff'],
output_names=['highpass'],
function=get_highpass),
name='gethighpass')
wf.connect(subjinfo, 'TR', gethighpass, 'TR')
wf.connect(gethighpass, 'highpass', preproc, 'inputspec.highpass')
"""
Setup a basic set of contrasts, a t-test per condition
"""
def get_contrasts(contrast_file, task_id, conds):
import numpy as np
import os
contrast_def = []
if os.path.exists(contrast_file):
with open(contrast_file, 'rt') as fp:
contrast_def.extend([
np.array(row.split()) for row in fp.readlines()
if row.strip()
])
contrasts = []
for row in contrast_def:
if row[0] != 'task%03d' % task_id:
continue
con = [
row[1], 'T', ['cond%03d' % (i + 1) for i in range(len(conds))],
row[2:].astype(float).tolist()
]
contrasts.append(con)
# add auto contrasts for each column
for i, cond in enumerate(conds):
con = [cond, 'T', ['cond%03d' % (i + 1)], [1]]
contrasts.append(con)
return contrasts
contrastgen = pe.Node(
niu.Function(
input_names=['contrast_file', 'task_id', 'conds'],
output_names=['contrasts'],
function=get_contrasts),
name='contrastgen')
art = pe.MapNode(
interface=ra.ArtifactDetect(
use_differences=[True, False],
use_norm=True,
norm_threshold=1,
zintensity_threshold=3,
parameter_source='FSL',
mask_type='file'),
iterfield=['realigned_files', 'realignment_parameters', 'mask_file'],
name="art")
modelspec = pe.Node(interface=model.SpecifyModel(), name="modelspec")
modelspec.inputs.input_units = 'secs'
def check_behav_list(behav, run_id, conds):
import numpy as np
num_conds = len(conds)
if isinstance(behav, (str, bytes)):
behav = [behav]
behav_array = np.array(behav).flatten()
num_elements = behav_array.shape[0]
return behav_array.reshape(int(num_elements / num_conds),
num_conds).tolist()
reshape_behav = pe.Node(
niu.Function(
input_names=['behav', 'run_id', 'conds'],
output_names=['behav'],
function=check_behav_list),
name='reshape_behav')
wf.connect(subjinfo, 'TR', modelspec, 'time_repetition')
wf.connect(datasource, 'behav', reshape_behav, 'behav')
wf.connect(subjinfo, 'run_id', reshape_behav, 'run_id')
wf.connect(subjinfo, 'conds', reshape_behav, 'conds')
wf.connect(reshape_behav, 'behav', modelspec, 'event_files')
wf.connect(subjinfo, 'TR', modelfit, 'inputspec.interscan_interval')
wf.connect(subjinfo, 'conds', contrastgen, 'conds')
if has_contrast:
wf.connect(datasource, 'contrasts', contrastgen, 'contrast_file')
else:
contrastgen.inputs.contrast_file = ''
wf.connect(infosource, 'task_id', contrastgen, 'task_id')
wf.connect(contrastgen, 'contrasts', modelfit, 'inputspec.contrasts')
wf.connect([(preproc, art,
[('outputspec.motion_parameters', 'realignment_parameters'),
('outputspec.realigned_files',
'realigned_files'), ('outputspec.mask', 'mask_file')]),
(preproc, modelspec,
[('outputspec.highpassed_files', 'functional_runs'),
('outputspec.motion_parameters', 'realignment_parameters')]),
(art, modelspec,
[('outlier_files', 'outlier_files')]), (modelspec, modelfit, [
('session_info', 'inputspec.session_info')
]), (preproc, modelfit, [('outputspec.highpassed_files',
'inputspec.functional_data')])])
# Comute TSNR on realigned data regressing polynomials upto order 2
tsnr = MapNode(TSNR(regress_poly=2), iterfield=['in_file'], name='tsnr')
wf.connect(preproc, "outputspec.realigned_files", tsnr, "in_file")
# Compute the median image across runs
calc_median = Node(CalculateMedian(), name='median')
wf.connect(tsnr, 'detrended_file', calc_median, 'in_files')
"""
Reorder the copes so that now it combines across runs
"""
def sort_copes(copes, varcopes, contrasts):
import numpy as np
if not isinstance(copes, list):
copes = [copes]
varcopes = [varcopes]
num_copes = len(contrasts)
n_runs = len(copes)
all_copes = np.array(copes).flatten()
all_varcopes = np.array(varcopes).flatten()
outcopes = all_copes.reshape(
int(len(all_copes) / num_copes), num_copes).T.tolist()
outvarcopes = all_varcopes.reshape(
int(len(all_varcopes) / num_copes), num_copes).T.tolist()
return outcopes, outvarcopes, n_runs
cope_sorter = pe.Node(
niu.Function(
input_names=['copes', 'varcopes', 'contrasts'],
output_names=['copes', 'varcopes', 'n_runs'],
function=sort_copes),
name='cope_sorter')
pickfirst = lambda x: x[0]
wf.connect(contrastgen, 'contrasts', cope_sorter, 'contrasts')
wf.connect([(preproc, fixed_fx,
[(('outputspec.mask', pickfirst),
'flameo.mask_file')]), (modelfit, cope_sorter,
[('outputspec.copes', 'copes')]),
(modelfit, cope_sorter, [('outputspec.varcopes', 'varcopes')]),
(cope_sorter, fixed_fx,
[('copes', 'inputspec.copes'), ('varcopes',
'inputspec.varcopes'),
('n_runs', 'l2model.num_copes')]), (modelfit, fixed_fx, [
('outputspec.dof_file', 'inputspec.dof_files'),
])])
wf.connect(calc_median, 'median_file', registration,
'inputspec.mean_image')
if subjects_dir:
wf.connect(infosource, 'subject_id', registration,
'inputspec.subject_id')
registration.inputs.inputspec.subjects_dir = subjects_dir
registration.inputs.inputspec.target_image = fsl.Info.standard_image(
'MNI152_T1_2mm_brain.nii.gz')
if target:
registration.inputs.inputspec.target_image = target
else:
wf.connect(datasource, 'anat', registration,
'inputspec.anatomical_image')
registration.inputs.inputspec.target_image = fsl.Info.standard_image(
'MNI152_T1_2mm.nii.gz')
registration.inputs.inputspec.target_image_brain = fsl.Info.standard_image(
'MNI152_T1_2mm_brain.nii.gz')
registration.inputs.inputspec.config_file = 'T1_2_MNI152_2mm'
def merge_files(copes, varcopes, zstats):
out_files = []
splits = []
out_files.extend(copes)
splits.append(len(copes))
out_files.extend(varcopes)
splits.append(len(varcopes))
out_files.extend(zstats)
splits.append(len(zstats))
return out_files, splits
mergefunc = pe.Node(
niu.Function(
input_names=['copes', 'varcopes', 'zstats'],
output_names=['out_files', 'splits'],
function=merge_files),
name='merge_files')
wf.connect([(fixed_fx.get_node('outputspec'), mergefunc, [
('copes', 'copes'),
('varcopes', 'varcopes'),
('zstats', 'zstats'),
])])
wf.connect(mergefunc, 'out_files', registration, 'inputspec.source_files')
def split_files(in_files, splits):
copes = in_files[:splits[0]]
varcopes = in_files[splits[0]:(splits[0] + splits[1])]
zstats = in_files[(splits[0] + splits[1]):]
return copes, varcopes, zstats
splitfunc = pe.Node(
niu.Function(
input_names=['in_files', 'splits'],
output_names=['copes', 'varcopes', 'zstats'],
function=split_files),
name='split_files')
wf.connect(mergefunc, 'splits', splitfunc, 'splits')
wf.connect(registration, 'outputspec.transformed_files', splitfunc,
'in_files')
if subjects_dir:
get_roi_mean = pe.MapNode(
fs.SegStats(default_color_table=True),
iterfield=['in_file'],
name='get_aparc_means')
get_roi_mean.inputs.avgwf_txt_file = True
wf.connect(
fixed_fx.get_node('outputspec'), 'copes', get_roi_mean, 'in_file')
wf.connect(registration, 'outputspec.aparc', get_roi_mean,
'segmentation_file')
get_roi_tsnr = pe.MapNode(
fs.SegStats(default_color_table=True),
iterfield=['in_file'],
name='get_aparc_tsnr')
get_roi_tsnr.inputs.avgwf_txt_file = True
wf.connect(tsnr, 'tsnr_file', get_roi_tsnr, 'in_file')
wf.connect(registration, 'outputspec.aparc', get_roi_tsnr,
'segmentation_file')
"""
Connect to a datasink
"""
def get_subs(subject_id, conds, run_id, model_id, task_id):
subs = [('_subject_id_%s_' % subject_id, '')]
subs.append(('_model_id_%d' % model_id, 'model%03d' % model_id))
subs.append(('task_id_%d/' % task_id, '/task%03d_' % task_id))
subs.append(('bold_dtype_mcf_mask_smooth_mask_gms_tempfilt_mean_warp',
'mean'))
subs.append(('bold_dtype_mcf_mask_smooth_mask_gms_tempfilt_mean_flirt',
'affine'))
for i in range(len(conds)):
subs.append(('_flameo%d/cope1.' % i, 'cope%02d.' % (i + 1)))
subs.append(('_flameo%d/varcope1.' % i, 'varcope%02d.' % (i + 1)))
subs.append(('_flameo%d/zstat1.' % i, 'zstat%02d.' % (i + 1)))
subs.append(('_flameo%d/tstat1.' % i, 'tstat%02d.' % (i + 1)))
subs.append(('_flameo%d/res4d.' % i, 'res4d%02d.' % (i + 1)))
subs.append(('_warpall%d/cope1_warp.' % i, 'cope%02d.' % (i + 1)))
subs.append(('_warpall%d/varcope1_warp.' % (len(conds) + i),
'varcope%02d.' % (i + 1)))
subs.append(('_warpall%d/zstat1_warp.' % (2 * len(conds) + i),
'zstat%02d.' % (i + 1)))
subs.append(('_warpall%d/cope1_trans.' % i, 'cope%02d.' % (i + 1)))
subs.append(('_warpall%d/varcope1_trans.' % (len(conds) + i),
'varcope%02d.' % (i + 1)))
subs.append(('_warpall%d/zstat1_trans.' % (2 * len(conds) + i),
'zstat%02d.' % (i + 1)))
subs.append(('__get_aparc_means%d/' % i, '/cope%02d_' % (i + 1)))
for i, run_num in enumerate(run_id):
subs.append(('__get_aparc_tsnr%d/' % i, '/run%02d_' % run_num))
subs.append(('__art%d/' % i, '/run%02d_' % run_num))
subs.append(('__dilatemask%d/' % i, '/run%02d_' % run_num))
subs.append(('__realign%d/' % i, '/run%02d_' % run_num))
subs.append(('__modelgen%d/' % i, '/run%02d_' % run_num))
subs.append(('/model%03d/task%03d/' % (model_id, task_id), '/'))
subs.append(('/model%03d/task%03d_' % (model_id, task_id), '/'))
subs.append(('_bold_dtype_mcf_bet_thresh_dil', '_mask'))
subs.append(('_output_warped_image', '_anat2target'))
subs.append(('median_flirt_brain_mask', 'median_brain_mask'))
subs.append(('median_bbreg_brain_mask', 'median_brain_mask'))
return subs
subsgen = pe.Node(
niu.Function(
input_names=[
'subject_id', 'conds', 'run_id', 'model_id', 'task_id'
],
output_names=['substitutions'],
function=get_subs),
name='subsgen')
wf.connect(subjinfo, 'run_id', subsgen, 'run_id')
datasink = pe.Node(interface=nio.DataSink(), name="datasink")
wf.connect(infosource, 'subject_id', datasink, 'container')
wf.connect(infosource, 'subject_id', subsgen, 'subject_id')
wf.connect(infosource, 'model_id', subsgen, 'model_id')
wf.connect(infosource, 'task_id', subsgen, 'task_id')
wf.connect(contrastgen, 'contrasts', subsgen, 'conds')
wf.connect(subsgen, 'substitutions', datasink, 'substitutions')
wf.connect([(fixed_fx.get_node('outputspec'), datasink,
[('res4d', 'res4d'), ('copes', 'copes'), ('varcopes',
'varcopes'),
('zstats', 'zstats'), ('tstats', 'tstats')])])
wf.connect([(modelfit.get_node('modelgen'), datasink, [
('design_cov', 'qa.model'),
('design_image', 'qa.model.@matrix_image'),
('design_file', 'qa.model.@matrix'),
])])
wf.connect([(preproc, datasink, [('outputspec.motion_parameters',
'qa.motion'), ('outputspec.motion_plots',
'qa.motion.plots'),
('outputspec.mask', 'qa.mask')])])
wf.connect(registration, 'outputspec.mean2anat_mask', datasink,
'qa.mask.mean2anat')
wf.connect(art, 'norm_files', datasink, 'qa.art.@norm')
wf.connect(art, 'intensity_files', datasink, 'qa.art.@intensity')
wf.connect(art, 'outlier_files', datasink, 'qa.art.@outlier_files')
wf.connect(registration, 'outputspec.anat2target', datasink,
'qa.anat2target')
wf.connect(tsnr, 'tsnr_file', datasink, 'qa.tsnr.@map')
if subjects_dir:
wf.connect(registration, 'outputspec.min_cost_file', datasink,
'qa.mincost')
wf.connect([(get_roi_tsnr, datasink, [('avgwf_txt_file', 'qa.tsnr'),
('summary_file',
'qa.tsnr.@summary')])])
wf.connect([(get_roi_mean, datasink, [('avgwf_txt_file', 'copes.roi'),
('summary_file',
'copes.roi.@summary')])])
wf.connect([(splitfunc, datasink, [
('copes', 'copes.mni'),
('varcopes', 'varcopes.mni'),
('zstats', 'zstats.mni'),
])])
wf.connect(calc_median, 'median_file', datasink, 'mean')
wf.connect(registration, 'outputspec.transformed_mean', datasink,
'mean.mni')
wf.connect(registration, 'outputspec.func2anat_transform', datasink,
'xfm.mean2anat')
wf.connect(registration, 'outputspec.anat2target_transform', datasink,
'xfm.anat2target')
"""
Set processing parameters
"""
preproc.inputs.inputspec.fwhm = fwhm
gethighpass.inputs.hpcutoff = hpcutoff
modelspec.inputs.high_pass_filter_cutoff = hpcutoff
modelfit.inputs.inputspec.bases = {'dgamma': {'derivs': use_derivatives}}
modelfit.inputs.inputspec.model_serial_correlations = True
modelfit.inputs.inputspec.film_threshold = 1000
datasink.inputs.base_directory = output_dir
return wf
Preliminaries
-------------
Setup any package specific configuration. The output file format for FSL
routines is being set to compressed NIFTI.
"""
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
level1_workflow = pe.Workflow(name='level1flow')
preproc = create_featreg_preproc(whichvol='first')
modelfit = create_modelfit_workflow()
fixed_fx = create_fixed_effects_flow()
"""
Add artifact detection and model specification nodes between the preprocessing
and modelfitting workflows.
"""
art = pe.MapNode(interface=ra.ArtifactDetect(use_differences=[True, False],
use_norm=True,
norm_threshold=1,
zintensity_threshold=3,
parameter_source='FSL',
mask_type='file'),
iterfield=['realigned_files', 'realignment_parameters', 'mask_file'],
name="art")
def analyze_openfmri_dataset(data_dir, subject=None, model_id=None, work_dir=None):
"""Analyzes an open fmri dataset
Parameters
----------
data_dir : str
Path to the base data directory
work_dir : str
Nipype working directory (defaults to cwd)
"""
"""
Load nipype workflows
"""
preproc = create_featreg_preproc(whichvol='first')
modelfit = create_modelfit_workflow()
fixed_fx = create_fixed_effects_flow()
"""
Remove the plotting connection so that plot iterables don't propagate
to the model stage
"""
preproc.disconnect(preproc.get_node('plot_motion'), 'out_file',
preproc.get_node('outputspec'), 'motion_plots')
"""
Set up openfmri data specific components
"""
subjects = [path.split(os.path.sep)[-1] for path in
glob(os.path.join(data_dir, 'sub*'))]
infosource = pe.Node(niu.IdentityInterface(fields=['subject_id',
'model_id']),
name='infosource')
if subject is None:
infosource.iterables = [('subject_id', subjects),
('model_id', [model_id])]
else:
infosource.iterables = [('subject_id',
[subjects[subjects.index(subject)]]),
('model_id', [model_id])]
subjinfo = pe.Node(niu.Function(input_names=['subject_id', 'base_dir',
'task_id', 'model_id'],
output_names=['run_id', 'conds', 'TR'],
function=get_subjectinfo),
name='subjectinfo')
subjinfo.inputs.base_dir = data_dir
"""
Return data components as anat, bold and behav
"""
datasource = pe.Node(nio.DataGrabber(infields=['subject_id', 'run_id',
'model_id'],
outfields=['anat', 'bold', 'behav']),
name='datasource')
datasource.inputs.base_directory = data_dir
datasource.inputs.template = '*'
datasource.inputs.field_template = {'anat': '%s/anatomy/highres001.nii.gz',
'bold': '%s/BOLD/task001_r*/bold.nii.gz',
'behav': ('%s/model/model%03d/onsets/task001_'
'run%03d/cond*.txt')}
datasource.inputs.template_args = {'anat': [['subject_id']],
'bold': [['subject_id']],
'behav': [['subject_id', 'model_id',
'run_id']]}
datasource.inputs.sorted = True
"""
Create meta workflow
"""
wf = pe.Workflow(name='openfmri')
wf.connect(infosource, 'subject_id', subjinfo, 'subject_id')
wf.connect(infosource, 'model_id', subjinfo, 'model_id')
wf.connect(infosource, 'subject_id', datasource, 'subject_id')
wf.connect(infosource, 'model_id', datasource, 'model_id')
wf.connect(subjinfo, 'run_id', datasource, 'run_id')
wf.connect([(datasource, preproc, [('bold', 'inputspec.func')]),
])
def get_highpass(TR, hpcutoff):
return hpcutoff / (2 * TR)
gethighpass = pe.Node(niu.Function(input_names=['TR', 'hpcutoff'],
output_names=['highpass'],
function=get_highpass),
name='gethighpass')
wf.connect(subjinfo, 'TR', gethighpass, 'TR')
wf.connect(gethighpass, 'highpass', preproc, 'inputspec.highpass')
"""
Setup a basic set of contrasts, a t-test per condition
"""
def get_contrasts(base_dir, model_id, conds):
import numpy as np
import os
contrast_file = os.path.join(base_dir, 'models', 'model%03d' % model_id,
'task_contrasts.txt')
contrast_def = np.genfromtxt(contrast_file, dtype=object)
contrasts = []
for row in contrast_def:
con = [row[0], 'T', ['cond%03d' % i for i in range(len(conds))],
row[1:].astype(float).tolist()]
contrasts.append(con)
return contrasts
contrastgen = pe.Node(niu.Function(input_names=['base_dir', 'model_id',
'conds'],
output_names=['contrasts'],
function=get_contrasts),
name='contrastgen')
contrastgen.inputs.base_dir = data_dir
art = pe.MapNode(interface=ra.ArtifactDetect(use_differences=[True, False],
use_norm=True,
norm_threshold=1,
zintensity_threshold=3,
parameter_source='FSL',
mask_type='file'),
iterfield=['realigned_files', 'realignment_parameters',
'mask_file'],
name="art")
modelspec = pe.Node(interface=model.SpecifyModel(),
name="modelspec")
modelspec.inputs.input_units = 'secs'
wf.connect(subjinfo, 'TR', modelspec, 'time_repetition')
wf.connect(datasource, 'behav', modelspec, 'event_files')
wf.connect(subjinfo, 'TR', modelfit, 'inputspec.interscan_interval')
wf.connect(subjinfo, 'conds', contrastgen, 'conds')
wf.connect(infosource, 'model_id', contrastgen, 'model_id')
wf.connect(contrastgen, 'contrasts', modelfit, 'inputspec.contrasts')
wf.connect([(preproc, art, [('outputspec.motion_parameters',
'realignment_parameters'),
('outputspec.realigned_files',
'realigned_files'),
('outputspec.mask', 'mask_file')]),
(preproc, modelspec, [('outputspec.highpassed_files',
'functional_runs'),
('outputspec.motion_parameters',
'realignment_parameters')]),
(art, modelspec, [('outlier_files', 'outlier_files')]),
(modelspec, modelfit, [('session_info',
'inputspec.session_info')]),
(preproc, modelfit, [('outputspec.highpassed_files',
'inputspec.functional_data')])
])
"""
Reorder the copes so that now it combines across runs
"""
def sort_copes(files):
numelements = len(files[0])
outfiles = []
for i in range(numelements):
outfiles.insert(i, [])
for j, elements in enumerate(files):
outfiles[i].append(elements[i])
return outfiles
def num_copes(files):
return len(files)
pickfirst = lambda x: x[0]
wf.connect([(preproc, fixed_fx, [(('outputspec.mask', pickfirst),
'flameo.mask_file')]),
(modelfit, fixed_fx, [(('outputspec.copes', sort_copes),
'inputspec.copes'),
('outputspec.dof_file',
'inputspec.dof_files'),
(('outputspec.varcopes',
sort_copes),
'inputspec.varcopes'),
(('outputspec.copes', num_copes),
'l2model.num_copes'),
])
])
"""
Connect to a datasink
"""
def get_subs(subject_id, conds):
subs = [('_subject_id_%s/' % subject_id, '')]
for i in range(len(conds)):
subs.append(('_flameo%d/cope1.' % i, 'cope%02d.' % (i + 1)))
subs.append(('_flameo%d/varcope1.' % i, 'varcope%02d.' % (i + 1)))
subs.append(('_flameo%d/zstat1.' % i, 'zstat%02d.' % (i + 1)))
subs.append(('_flameo%d/tstat1.' % i, 'tstat%02d.' % (i + 1)))
subs.append(('_flameo%d/res4d.' % i, 'res4d%02d.' % (i + 1)))
return subs
subsgen = pe.Node(niu.Function(input_names=['subject_id', 'conds'],
output_names=['substitutions'],
function=get_subs),
name='subsgen')
datasink = pe.Node(interface=nio.DataSink(),
name="datasink")
wf.connect(infosource, 'subject_id', datasink, 'container')
wf.connect(infosource, 'subject_id', subsgen, 'subject_id')
wf.connect(subjinfo, 'conds', subsgen, 'conds')
wf.connect(subsgen, 'substitutions', datasink, 'substitutions')
wf.connect([(fixed_fx.get_node('outputspec'), datasink,
[('res4d', 'res4d'),
('copes', 'copes'),
('varcopes', 'varcopes'),
('zstats', 'zstats'),
('tstats', 'tstats')])
])
"""
Set processing parameters
"""
hpcutoff = 120.
subjinfo.inputs.task_id = 1
preproc.inputs.inputspec.fwhm = 6.0
gethighpass.inputs.hpcutoff = hpcutoff
modelspec.inputs.high_pass_filter_cutoff = hpcutoff
modelfit.inputs.inputspec.bases = {'dgamma': {'derivs': True}}
modelfit.inputs.inputspec.model_serial_correlations = True
modelfit.inputs.inputspec.film_threshold = 1000
if work_dir is None:
work_dir = os.path.join(os.getcwd(), 'working')
wf.base_dir = work_dir
datasink.inputs.base_directory = os.path.join(work_dir, 'output')
wf.config['execution'] = dict(crashdump_dir=os.path.join(work_dir,
'crashdumps'),
stop_on_first_crash=True)
wf.run('MultiProc', plugin_args={'n_procs': 2})
def create_modelfit_workflow_bfsl(name='modelfit_workflow_bfsl'):
inputspec = pe.Node(util.IdentityInterface(fields=['functional_runs',
'bases',
'bfsl_files',
'contrasts',
'interscan_interval',
'film_threshold',
'model_serial_correlations',
'highpass_filter',
'mask',
'realignment_parameters'],),
name='inputspec')
workflow = pe.Workflow(name=name)
modelfit_workflow = create_modelfit_workflow()
inputspec.inputs.bases = {'dgamma': {'derivs': True}}
inputspec.inputs.film_threshold = 1000
inputspec.inputs.interscan_interval = 2.0
inputspec.inputs.model_serial_correlations = True
inputspec.inputs.highpass_filter = 128
for field in ['bases', 'contrasts', 'film_threshold', 'interscan_interval', 'model_serial_correlations']:
workflow.connect(inputspec, field, modelfit_workflow, 'inputspec.%s' % field)
from nipype.algorithms.modelgen import SpecifyModel
from nipype.interfaces import fsl
specifymodel = pe.Node(SpecifyModel(), name='specifymodel')
specifymodel.inputs.input_units = 'secs'
def get_highpas_filter_cutoff(hz, tr):
return float(hz) / (tr * 2)
get_highpas_filter_cutoff_node = pe.Node(util.Function(function=get_highpas_filter_cutoff,
input_names=['hz', 'tr'],
output_names='cutoff'),
name='get_highpas_filter_cutoff_node')
workflow.connect(inputspec, 'interscan_interval', get_highpas_filter_cutoff_node, 'tr')
workflow.connect(inputspec, 'highpass_filter', get_highpas_filter_cutoff_node, 'hz')
workflow.connect(get_highpas_filter_cutoff_node, 'cutoff', specifymodel, 'high_pass_filter_cutoff')
workflow.connect(inputspec, 'interscan_interval', specifymodel, 'time_repetition')
workflow.connect(inputspec, 'bfsl_files', specifymodel, 'event_files')
workflow.connect(inputspec, 'functional_runs', specifymodel, 'functional_runs')
workflow.connect(inputspec, 'realignment_parameters', specifymodel, 'realignment_parameters')
workflow.connect(specifymodel, 'session_info', modelfit_workflow, 'inputspec.session_info')
workflow.connect(inputspec, 'functional_runs', modelfit_workflow, 'inputspec.functional_data')
fixedfx = create_fixed_effects_flow()
workflow.connect(inputspec, 'mask', fixedfx, 'flameo.mask_file')
def num_copes(files):
return len(files)
def transpose_copes(copes):
import numpy as np
return np.array(copes).T.tolist()
workflow.connect([(modelfit_workflow, fixedfx,
[(('outputspec.copes', transpose_copes), 'inputspec.copes'),
(('outputspec.varcopes', transpose_copes), 'inputspec.varcopes'),
('outputspec.dof_file', 'inputspec.dof_files'),
(('outputspec.copes', num_copes), 'l2model.num_copes')])])
ztopval = pe.MapNode(interface=fsl.ImageMaths(op_string='-ztop',
suffix='_pval'),
nested=True,
iterfield=['in_file'],
name='ztop',)
fdr_workflow = create_fdr_threshold_workflow()
workflow.connect([
(fixedfx, ztopval,
[('outputspec.zstats', 'in_file'),]),
(fixedfx, fdr_workflow,
[('outputspec.zstats', 'inputspec.z_stats'),]),
(ztopval, fdr_workflow,
[('out_file', 'inputspec.p_values'),]),
(inputspec, fdr_workflow,
[('mask', 'inputspec.mask'),]),
])
outputpsec = pe.Node(util.IdentityInterface(fields=['zstats', 'level2_copes', 'level2_varcopes', 'level2_tdof', 'thresholded_zstats']), name='outputspec')
workflow.connect(fixedfx, 'outputspec.zstats', outputpsec, 'zstats')
workflow.connect(fixedfx, 'outputspec.copes', outputpsec, 'level2_copes')
workflow.connect(fixedfx, 'outputspec.varcopes', outputpsec, 'level2_varcopes')
workflow.connect(fixedfx, 'flameo.tdof', outputpsec, 'level2_tdof')
workflow.connect(fdr_workflow, 'outputspec.thresholded_z_stats', outputpsec, 'thresholded_z_stats')
return workflow
def create_random_effects_workflow(name='randomfx'):
inputspec = pe.Node(util.IdentityInterface(fields=['cope_files',
'varcope_files',
'tdof_files',
'mask_file',
'fdr_q']),
name='inputspec')
inputspec.inputs.fdr_q = 0.05
workflow = pe.Workflow(name=name)
fixedfx_flow = create_fixed_effects_flow()
def num_copes(files):
return len(files)
def listify(x):
return [x]
workflow.connect(inputspec, ('cope_files', listify), fixedfx_flow, 'inputspec.copes')
workflow.connect(inputspec, ('varcope_files', listify), fixedfx_flow, 'inputspec.varcopes')
workflow.connect(inputspec, ('varcope_files', num_copes), fixedfx_flow, 'l2model.num_copes')
workflow.connect(inputspec, 'mask_file', fixedfx_flow, 'flameo.mask_file')
fixedfx_flow.inputs.flameo.run_mode = 'flame1'
fixedfx_flow.disconnect([(fixedfx_flow.get_node('inputspec'), fixedfx_flow.get_node('gendofvolume'), [('dof_files', 'dof_files')]),
(fixedfx_flow.get_node('copemerge'), fixedfx_flow.get_node('gendofvolume'), [('merged_file', 'cope_files')]),
(fixedfx_flow.get_node('gendofvolume'), fixedfx_flow.get_node('flameo'), [('dof_volume', 'dof_var_cope_file')])])
fixedfx_flow.remove_nodes([fixedfx_flow.get_node('gendofvolume')])
tdof_merge = pe.Node(interface=fsl.Merge(dimension='t'), name="tdof_merge")
workflow.connect(inputspec, 'tdof_files', tdof_merge, 'in_files')
workflow.connect(tdof_merge, 'merged_file', fixedfx_flow, 'flameo.dof_var_cope_file')
ztopval = pe.MapNode(interface=fsl.ImageMaths(op_string='-ztop',
suffix='_pval'),
iterfield=['in_file'],
nested=True,
name='ztop',)
fdr_workflow = create_fdr_threshold_workflow()
workflow.connect([
(fixedfx_flow, ztopval,
[('outputspec.zstats', 'in_file'),]),
(fixedfx_flow, fdr_workflow,
[('outputspec.zstats', 'inputspec.z_stats'),]),
(ztopval, fdr_workflow,
[('out_file', 'inputspec.p_values'),]),
])
workflow.connect(inputspec, 'mask_file', fdr_workflow, 'inputspec.mask')
workflow.connect(inputspec, 'fdr_q', fdr_workflow, 'inputspec.q')
cluster = pe.MapNode(fsl.Cluster(), iterfield=['in_file'], name='cluster')
cluster.inputs.threshold = 2.0
cluster.inputs.out_threshold_file = True
cluster.inputs.out_localmax_txt_file = True
workflow.connect(fdr_workflow, 'outputspec.thresholded_z_stats', cluster, 'in_file')
outputspec = pe.Node(util.IdentityInterface(fields=['zstats', 'thresholded_z_stats', 'txt_index_file']), name='outputspec')
workflow.connect(fixedfx_flow, 'outputspec.zstats', outputspec, 'zstats')
workflow.connect(fdr_workflow, 'outputspec.thresholded_z_stats', outputspec, 'thresholded_z_stats')
workflow.connect(cluster, 'localmax_txt_file', outputspec, 'txt_index_file')
return workflow
def create_workflow(out_label, contrasts_name, RegSpace):
level2_workflow = pe.Workflow(name='level2flow')
level2_workflow.base_dir = os.path.abspath('./workingdirs/level2flow/' +
contrasts_name + '/' +
RegSpace + '/level2/' +
out_label)
# ===================================================================
# _____ _
# |_ _| | |
# | | _ __ _ __ _ _| |_
# | | | '_ \| '_ \| | | | __|
# _| |_| | | | |_) | |_| | |_
# |_____|_| |_| .__/ \__,_|\__|
# | |
# |_|
# ===================================================================
# ------------------ Specify variables
inputnode = pe.Node(niu.IdentityInterface(fields=[
'ref_funcmask',
'copes',
'dof_file',
'varcopes',
]),
name="inputspec")
# -------------------------------------------------------------------
# /~_ _ _ _ _. _ _ . _ _ |. _ _
# \_/(/_| |(/_| |(_ |_)||_)(/_||| |(/_
# | |
# -------------------------------------------------------------------
"""
Preliminaries
-------------
Setup any package specific configuration. The output file format for FSL
routines is being set to compressed NIFTI.
"""
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
fixed_fx = fslflows.create_fixed_effects_flow()
def sort_copes(files):
""" Sort by copes and the runs, ie.
[[cope1_run1, cope1_run2], [cope2_run1, cope2_run2]]
"""
assert files[0] is not str
numcopes = len(files[0])
assert numcopes > 1
outfiles = []
for i in range(numcopes):
outfiles.insert(i, [])
for j, elements in enumerate(files):
outfiles[i].append(elements[i])
return outfiles
def num_copes(files):
return len(files)
# Level2 fixed effects
level2_workflow.connect([(inputnode, fixed_fx, [
('ref_funcmask', 'flameo.mask_file'),
(('copes', sort_copes), 'inputspec.copes'),
('dof_file', 'inputspec.dof_files'),
(('varcopes', sort_copes), 'inputspec.varcopes'),
(('copes', num_copes), 'l2model.num_copes'),
])])
# ===================================================================
# ____ _ _
# / __ \ | | | |
# | | | |_ _| |_ _ __ _ _| |_
# | | | | | | | __| '_ \| | | | __|
# | |__| | |_| | |_| |_) | |_| | |_
# \____/ \__,_|\__| .__/ \__,_|\__|
# | |
# |_|
# ===================================================================
# Datasink
outputfiles = pe.Node(
nio.DataSink(base_directory=ds_root,
container='derivatives/modelfit/' + contrasts_name + '/' +
RegSpace + '/level2/' + out_label,
parameterization=True),
name="output_files")
# Use the following DataSink output substitutions
outputfiles.inputs.substitutions = [
('subject_id_', 'sub-'),
('session_id_', 'ses-'),
]
# Put result into a BIDS-like format
outputfiles.inputs.regexp_substitutions = [
(r'_ses-([a-zA-Z0-9]+)_sub-([a-zA-Z0-9]+)', r'sub-\2/ses-\1'),
(r'_refsub([a-zA-Z0-9]+)', r''),
]
level2_workflow.connect([
(fixed_fx, outputfiles, [
('outputspec.res4d', 'fx.res4d'),
('outputspec.copes', 'fx.copes'),
('outputspec.varcopes', 'fx.varcopes'),
('outputspec.zstats', 'fx.zstats'),
('outputspec.tstats', 'fx.tstats'),
]),
])
return (level2_workflow)
