def ms_anat(settings=None, subject_id=None, session_id=None, run_id=None):
""" Multi-subject anatomical workflow wrapper """
# Run single subject mode if only one subject id is provided
if subject_id is not None and isinstance(subject_id, string_types):
subject_id = [subject_id]
sub_list = gather_bids_data(settings['bids_dir'],
subject_inclusion=subject_id,
include_types=['anat'])
if session_id is not None:
sub_list = [s for s in sub_list if s[1] == session_id]
if run_id is not None:
sub_list = [s for s in sub_list if s[2] == run_id]
if not sub_list:
return None
inputnode = pe.Node(niu.IdentityInterface(fields=['data']),
name='inputnode')
inputnode.iterables = [('data', [list(s) for s in sub_list])]
anat_qc = anat_qc_workflow(settings=settings)
anat_qc.inputs.inputnode.bids_dir = settings['bids_dir']
dsplit = pe.Node(niu.Split(splits=[1, 1, 1], squeeze=True),
name='datasplit')
workflow = pe.Workflow(name='anatMRIQC')
workflow.connect([
(inputnode, dsplit, [('data', 'inlist')]),
(dsplit, anat_qc, [('out1', 'inputnode.subject_id'),
('out2', 'inputnode.session_id'),
('out3', 'inputnode.run_id')])
])
return workflow
def build_workflow(dataset, mod, settings=None):
""" Multi-subject anatomical workflow wrapper """
if mod == 'bold':
workflow = fmri_qc_workflow(dataset, settings=settings)
elif mod == 'T1w':
workflow = anat_qc_workflow(dataset, mod='T1w', settings=settings)
elif mod == 'T2w':
workflow = anat_qc_workflow(dataset, mod='T2w', settings=settings)
else:
raise NotImplementedError('Unknown workflow type "%s"' % mod)
workflow.base_dir = settings['work_dir']
if settings.get('write_graph', False):
workflow.write_graph()
return workflow
def ms_anat(settings=None, subject_id=None, session_id=None, run_id=None):
""" Multi-subject anatomical workflow wrapper """
# Run single subject mode if only one subject id is provided
if subject_id is not None and isinstance(subject_id, string_types):
subject_id = [subject_id]
sub_list = gather_bids_data(settings['bids_root'],
subject_inclusion=subject_id,
include_types=['anat'])
if session_id is not None:
sub_list = [s for s in sub_list if s[1] == session_id]
if run_id is not None:
sub_list = [s for s in sub_list if s[2] == run_id]
if not sub_list:
return None
inputnode = pe.Node(niu.IdentityInterface(fields=['data']),
name='inputnode')
inputnode.iterables = [('data', [list(s) for s in sub_list])]
anat_qc = anat_qc_workflow(settings=settings)
anat_qc.inputs.inputnode.bids_root = settings['bids_root']
dsplit = pe.Node(niu.Split(splits=[1, 1, 1], squeeze=True),
name='datasplit')
workflow = pe.Workflow(name='anatMRIQC')
workflow.connect([
(inputnode, dsplit, [('data', 'inlist')]),
(dsplit, anat_qc, [('out1', 'inputnode.subject_id'),
('out2', 'inputnode.session_id'),
('out3', 'inputnode.run_id')])
])
return workflow
def build_workflow(dataset, qctype, settings=None):
""" Multi-subject anatomical workflow wrapper """
if qctype.startswith('func'):
workflow = fmri_qc_workflow(dataset, settings=settings)
elif qctype.startswith('anat'):
workflow = anat_qc_workflow(dataset, settings=settings)
else:
raise NotImplementedError('Unknown workflow type "%s"' % qctype)
workflow.base_dir = settings['work_dir']
if settings.get('write_graph', False):
workflow.write_graph()
return workflow
def init_mriqc_wf():
"""Create a multi-subject MRIQC workflow."""
from mriqc import config
# Create parent workflow
workflow = Workflow(name="mriqc_wf")
workflow.base_dir = config.execution.work_dir
# Create fMRI QC workflow
if FMRI_KEY in config.workflow.inputs:
workflow.add_nodes([fmri_qc_workflow()])
# Create sMRI QC workflow
input_keys = config.workflow.inputs.keys()
anatomical_flag = any(key in input_keys for key in ANATOMICAL_KEYS)
if anatomical_flag:
workflow.add_nodes([anat_qc_workflow()])
# Return non-empty workflow, else None
if workflow._get_all_nodes():
return workflow
import os.path as op
from mriqc.workflows.anatomical import anat_qc_workflow
from mriqc.testing import mock_config
datadir = '/home/kilimanjaro2/Research/monkeyStuff/bidsData/'
with mock_config():
wf = anat_qc_workflow(
[op.join(datadir, 'sub-100/anat/sub-100_T1w.nii.gz')])
wf.run()
wf = anat_qc_workflow(
[op.join(datadir, 'sub-101/anat/sub-101_T1w.nii.gz')])
wf.run()
wf = anat_qc_workflow(
[op.join(datadir, 'sub-102/anat/sub-102_T1w.nii.gz')])
wf.run()
# wf = anat_qc_workflow([op.join(datadir, 'sub-152/anat/sub-152_T1w.nii.gz')])
# wf.run()
# wf = anat_qc_workflow([op.join(datadir, 'sub-154/anat/sub-154_T1w.nii.gz')])
# wf.run()
# wf = anat_qc_workflow([op.join(datadir, 'sub-156/anat/sub-156_T1w.nii.gz')])
# wf.run()
# wf = anat_qc_workflow([op.join(datadir, 'sub-158/anat/sub-158_T1w.nii.gz')])
# wf.run()
# wf = anat_qc_workflow([op.join(datadir, 'sub-160/anat/sub-160_T1w.nii.gz')])
# wf.run()
# wf = anat_qc_workflow([op.join(datadir, 'sub-162/anat/sub-162_T1w.nii.gz')])
# wf.run()
# wf = anat_qc_workflow([op.join(datadir, 'sub-164/anat/sub-164_T1w.nii.gz')])
# wf.run()
import os.path as op
from mriqc.workflows.anatomical import anat_qc_workflow
from mriqc.testing import mock_config
datadir = '/home/kilimanjaro2/Research/monkeyStuff/bidsData/'
with mock_config():
wf = anat_qc_workflow(
[op.join(datadir, 'sub-103/anat/sub-103_T1w.nii.gz')])
wf.run()
wf = anat_qc_workflow(
[op.join(datadir, 'sub-104/anat/sub-104_T1w.nii.gz')])
wf.run()