# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
#
# Copyright 2021 The NiPreps Developers <nipreps@gmail.com>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# We support and encourage derived works from this project, please read
# about our expectations at
#
# https://www.nipreps.org/community/licensing/
#
"""*sMRIPrep* base processing workflows."""
import os
import sys
from copy import deepcopy
from nipype import __version__ as nipype_ver
from nipype.interfaces import utility as niu
from nipype.pipeline import engine as pe
from niworkflows.engine.workflows import LiterateWorkflow as Workflow
from niworkflows.interfaces.bids import BIDSDataGrabber, BIDSFreeSurferDir, BIDSInfo
from niworkflows.utils.bids import collect_data
from niworkflows.utils.misc import fix_multi_T1w_source_name
from ..__about__ import __version__
from ..interfaces import DerivativesDataSink
from .anatomical import init_anat_preproc_wf
[docs]
def init_smriprep_wf(
*,
sloppy,
debug,
derivatives,
freesurfer,
fs_subjects_dir,
hires,
fs_no_resume,
layout,
longitudinal,
low_mem,
msm_sulc,
omp_nthreads,
output_dir,
run_uuid,
skull_strip_mode,
skull_strip_fixed_seed,
skull_strip_template,
spaces,
subject_list,
work_dir,
bids_filters,
cifti_output,
):
"""
Create the execution graph of *sMRIPrep*, with a sub-workflow for each subject.
If FreeSurfer's ``recon-all`` is to be run, a FreeSurfer derivatives folder is
created and populated with any needed template subjects.
Workflow Graph
.. workflow::
:graph2use: orig
:simple_form: yes
import os
from collections import namedtuple
BIDSLayout = namedtuple('BIDSLayout', ['root'])
os.environ['FREESURFER_HOME'] = os.getcwd()
from smriprep.workflows.base import init_smriprep_wf
from niworkflows.utils.spaces import SpatialReferences, Reference
spaces = SpatialReferences(spaces=['MNI152NLin2009cAsym', 'fsaverage5'])
spaces.checkpoint()
wf = init_smriprep_wf(
sloppy=False,
debug=False,
derivatives=[],
freesurfer=True,
fs_subjects_dir=None,
hires=True,
fs_no_resume=False,
layout=BIDSLayout('.'),
longitudinal=False,
low_mem=False,
msm_sulc=False,
omp_nthreads=1,
output_dir='.',
run_uuid='testrun',
skull_strip_fixed_seed=False,
skull_strip_mode='force',
skull_strip_template=Reference('OASIS30ANTs'),
spaces=spaces,
subject_list=['smripreptest'],
work_dir='.',
bids_filters=None,
cifti_output=None,
)
Parameters
----------
sloppy: :obj:`bool`
Quick, impercise operations. Used to decrease workflow duration.
debug : :obj:`bool`
Enable debugging outputs
derivatives : :obj:`list` of directories
Fast-track the workflow by searching for existing derivatives.
freesurfer : :obj:`bool`
Enable FreeSurfer surface reconstruction (may increase runtime)
fs_subjects_dir : os.PathLike or None
Use existing FreeSurfer subjects directory if provided
hires : :obj:`bool`
Enable sub-millimeter preprocessing in FreeSurfer
layout : BIDSLayout object
BIDS dataset layout
longitudinal : :obj:`bool`
Treat multiple sessions as longitudinal (may increase runtime)
See sub-workflows for specific differences
low_mem : :obj:`bool`
Write uncompressed .nii files in some cases to reduce memory usage
msm_sulc : :obj:`bool`
Run Multimodal Surface Matching with sulcal depth maps
omp_nthreads : :obj:`int`
Maximum number of threads an individual process may use
output_dir : :obj:`str`
Directory in which to save derivatives
run_uuid : :obj:`str`
Unique identifier for execution instance
skull_strip_fixed_seed : :obj:`bool`
Do not use a random seed for skull-stripping - will ensure
run-to-run replicability when used with --omp-nthreads 1
skull_strip_mode : :obj:`str`
Determiner for T1-weighted skull stripping (`force` ensures skull stripping,
`skip` ignores skull stripping, and `auto` automatically ignores skull stripping
if pre-stripped brains are detected).
skull_strip_template : :py:class:`~niworkflows.utils.spaces.Reference`
Spatial reference to use in atlas-based brain extraction.
spaces : :py:class:`~niworkflows.utils.spaces.SpatialReferences`
Object containing standard and nonstandard space specifications.
subject_list : :obj:`list`
List of subject labels
work_dir : :obj:`str`
Directory in which to store workflow execution state and
temporary files
bids_filters : dict
Provides finer specification of the pipeline input files through pybids entities filters.
A dict with the following structure {<suffix>:{<entity>:<filter>,...},...}
"""
smriprep_wf = Workflow(name='smriprep_wf')
smriprep_wf.base_dir = work_dir
if freesurfer:
fsdir = pe.Node(
BIDSFreeSurferDir(
derivatives=output_dir,
freesurfer_home=os.getenv('FREESURFER_HOME'),
spaces=spaces.get_fs_spaces(),
),
name='fsdir_run_%s' % run_uuid.replace('-', '_'),
run_without_submitting=True,
)
if fs_subjects_dir is not None:
fsdir.inputs.subjects_dir = str(fs_subjects_dir.absolute())
for subject_id in subject_list:
single_subject_wf = init_single_subject_wf(
sloppy=sloppy,
debug=debug,
freesurfer=freesurfer,
derivatives=derivatives,
hires=hires,
fs_no_resume=fs_no_resume,
layout=layout,
longitudinal=longitudinal,
low_mem=low_mem,
msm_sulc=msm_sulc,
name='single_subject_%s_wf' % subject_id,
omp_nthreads=omp_nthreads,
output_dir=output_dir,
skull_strip_fixed_seed=skull_strip_fixed_seed,
skull_strip_mode=skull_strip_mode,
skull_strip_template=skull_strip_template,
spaces=spaces,
subject_id=subject_id,
bids_filters=bids_filters,
cifti_output=cifti_output,
)
single_subject_wf.config['execution']['crashdump_dir'] = os.path.join(
output_dir, 'smriprep', 'sub-' + subject_id, 'log', run_uuid
)
for node in single_subject_wf._get_all_nodes():
node.config = deepcopy(single_subject_wf.config)
if freesurfer:
smriprep_wf.connect(fsdir, 'subjects_dir', single_subject_wf, 'inputnode.subjects_dir')
else:
smriprep_wf.add_nodes([single_subject_wf])
return smriprep_wf
[docs]
def init_single_subject_wf(
*,
sloppy,
debug,
derivatives,
freesurfer,
hires,
fs_no_resume,
layout,
longitudinal,
low_mem,
msm_sulc,
name,
omp_nthreads,
output_dir,
skull_strip_fixed_seed,
skull_strip_mode,
skull_strip_template,
spaces,
subject_id,
bids_filters,
cifti_output,
):
"""
Create a single subject workflow.
This workflow organizes the preprocessing pipeline for a single subject.
It collects and reports information about the subject, and prepares
sub-workflows to perform anatomical and functional preprocessing.
Anatomical preprocessing is performed in a single workflow, regardless of
the number of sessions.
Functional preprocessing is performed using a separate workflow for each
individual BOLD series.
Workflow Graph
.. workflow::
:graph2use: orig
:simple_form: yes
from collections import namedtuple
from niworkflows.utils.spaces import SpatialReferences, Reference
from smriprep.workflows.base import init_single_subject_wf
BIDSLayout = namedtuple('BIDSLayout', ['root'])
spaces = SpatialReferences(spaces=['MNI152NLin2009cAsym', 'fsaverage5'])
spaces.checkpoint()
wf = init_single_subject_wf(
sloppy=False,
debug=False,
freesurfer=True,
derivatives=[],
hires=True,
fs_no_resume=False,
layout=BIDSLayout('.'),
longitudinal=False,
low_mem=False,
msm_sulc=False,
name='single_subject_wf',
omp_nthreads=1,
output_dir='.',
skull_strip_fixed_seed=False,
skull_strip_mode='force',
skull_strip_template=Reference('OASIS30ANTs'),
spaces=spaces,
subject_id='test',
bids_filters=None,
cifti_output=None,
)
Parameters
----------
sloppy: :obj:`bool`
Quick, impercise operations. Used to decrease workflow duration.
debug : :obj:`bool`
Enable debugging outputs
derivatives : :obj:`list` of directories
Fast-track the workflow by searching for existing derivatives.
freesurfer : :obj:`bool`
Enable FreeSurfer surface reconstruction (may increase runtime)
hires : :obj:`bool`
Enable sub-millimeter preprocessing in FreeSurfer
fs_no_resume : bool
Adjust pipeline to reuse base template
of an existing longitudinal freesurfer output
layout : BIDSLayout object
BIDS dataset layout
longitudinal : :obj:`bool`
Treat multiple sessions as longitudinal (may increase runtime)
See sub-workflows for specific differences
low_mem : :obj:`bool`
Write uncompressed .nii files in some cases to reduce memory usage
name : :obj:`str`
Name of workflow
omp_nthreads : :obj:`int`
Maximum number of threads an individual process may use
output_dir : :obj:`str`
Directory in which to save derivatives
skull_strip_fixed_seed : :obj:`bool`
Do not use a random seed for skull-stripping - will ensure
run-to-run replicability when used with --omp-nthreads 1
skull_strip_mode : :obj:`str`
Determiner for T1-weighted skull stripping (`force` ensures skull stripping,
`skip` ignores skull stripping, and `auto` automatically ignores skull stripping
if pre-stripped brains are detected).
skull_strip_template : :py:class:`~niworkflows.utils.spaces.Reference`
Spatial reference to use in atlas-based brain extraction.
spaces : :py:class:`~niworkflows.utils.spaces.SpatialReferences`
Object containing standard and nonstandard space specifications.
subject_id : :obj:`str`
List of subject labels
bids_filters : dict
Provides finer specification of the pipeline input files through pybids entities filters.
A dict with the following structure {<suffix>:{<entity>:<filter>,...},...}
Inputs
------
subjects_dir
FreeSurfer SUBJECTS_DIR
"""
from ..interfaces.reports import AboutSummary, SubjectSummary
if name in ('single_subject_wf', 'single_subject_smripreptest_wf'):
# for documentation purposes
subject_data = {
't1w': ['/completely/made/up/path/sub-01_T1w.nii.gz'],
't2w': [],
'flair': [],
}
else:
subject_data = collect_data(layout, subject_id, bids_filters=bids_filters)[0]
if not subject_data['t1w']:
raise Exception(
f'No T1w images found for participant {subject_id}. All workflows require T1w images.'
)
workflow = Workflow(name=name)
workflow.__desc__ = f"""
Results included in this manuscript come from preprocessing
performed using *sMRIPprep* {__version__}
(@fmriprep1; @fmriprep2; RRID:SCR_016216),
which is based on *Nipype* {nipype_ver}
(@nipype1; @nipype2; RRID:SCR_002502).
"""
workflow.__postdesc__ = """
For more details of the pipeline, see [the section corresponding
to workflows in *sMRIPrep*'s documentation]\
(https://smriprep.readthedocs.io/en/latest/workflows.html \
"sMRIPrep's documentation").
### References
"""
from ..utils.bids import collect_derivatives
deriv_cache = {}
std_spaces = spaces.get_spaces(nonstandard=False, dim=(3,))
std_spaces.append('fsnative')
for deriv_dir in derivatives:
deriv_cache.update(collect_derivatives(deriv_dir, subject_id, std_spaces))
inputnode = pe.Node(niu.IdentityInterface(fields=['subjects_dir']), name='inputnode')
bidssrc = pe.Node(BIDSDataGrabber(subject_data=subject_data, anat_only=True), name='bidssrc')
bids_info = pe.Node(
BIDSInfo(bids_dir=layout.root), name='bids_info', run_without_submitting=True
)
summary = pe.Node(
SubjectSummary(output_spaces=spaces.get_spaces(nonstandard=False)),
name='summary',
run_without_submitting=True,
)
about = pe.Node(
AboutSummary(version=__version__, command=' '.join(sys.argv)),
name='about',
run_without_submitting=True,
)
ds_report_summary = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
dismiss_entities=('session',),
desc='summary',
datatype='figures',
),
name='ds_report_summary',
run_without_submitting=True,
)
ds_report_about = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
dismiss_entities=('session',),
desc='about',
datatype='figures',
),
name='ds_report_about',
run_without_submitting=True,
)
# Preprocessing of T1w (includes registration to MNI)
anat_preproc_wf = init_anat_preproc_wf(
bids_root=layout.root,
sloppy=sloppy,
debug=debug,
precomputed=deriv_cache,
freesurfer=freesurfer,
hires=hires,
fs_no_resume=fs_no_resume,
longitudinal=longitudinal,
msm_sulc=msm_sulc,
name='anat_preproc_wf',
t1w=subject_data['t1w'],
t2w=subject_data['t2w'],
flair=subject_data['flair'],
omp_nthreads=omp_nthreads,
output_dir=output_dir,
skull_strip_fixed_seed=skull_strip_fixed_seed,
skull_strip_mode=skull_strip_mode,
skull_strip_template=skull_strip_template,
spaces=spaces,
cifti_output=cifti_output,
)
# fmt:off
workflow.connect([
(inputnode, anat_preproc_wf, [('subjects_dir', 'inputnode.subjects_dir')]),
(bidssrc, bids_info, [(('t1w', fix_multi_T1w_source_name), 'in_file')]),
(inputnode, summary, [('subjects_dir', 'subjects_dir')]),
(bidssrc, summary, [('t1w', 't1w'),
('t2w', 't2w')]),
(bids_info, summary, [('subject', 'subject_id')]),
(bids_info, anat_preproc_wf, [(('subject', _prefix), 'inputnode.subject_id')]),
(bidssrc, anat_preproc_wf, [('t1w', 'inputnode.t1w'),
('t2w', 'inputnode.t2w'),
('roi', 'inputnode.roi'),
('flair', 'inputnode.flair')]),
(bidssrc, ds_report_summary, [(('t1w', fix_multi_T1w_source_name), 'source_file')]),
(summary, ds_report_summary, [('out_report', 'in_file')]),
(bidssrc, ds_report_about, [(('t1w', fix_multi_T1w_source_name), 'source_file')]),
(about, ds_report_about, [('out_report', 'in_file')]),
])
# fmt:on
return workflow
def _prefix(subid):
if subid.startswith('sub-'):
return subid
return '-'.join(('sub', subid))