def init_fmriprep_wf():
"""
Build *fMRIPrep*'s pipeline.
This workflow organizes the execution of FMRIPREP, with a sub-workflow for
each subject.
If FreeSurfer's ``recon-all`` is to be run, a corresponding folder is created
and populated with any needed template subjects under the derivatives folder.
Workflow Graph
.. workflow::
:graph2use: orig
:simple_form: yes
from fmriprep.workflows.tests import mock_config
from fmriprep.workflows.base import init_fmriprep_wf
with mock_config():
wf = init_fmriprep_wf()
"""
from niworkflows.engine.workflows import LiterateWorkflow as Workflow
from niworkflows.interfaces.bids import BIDSFreeSurferDir
fmriprep_wf = Workflow(name='fmriprep_wf')
fmriprep_wf.base_dir = config.execution.work_dir
freesurfer = config.workflow.run_reconall
if freesurfer:
fsdir = pe.Node(
BIDSFreeSurferDir(derivatives=config.execution.output_dir,
freesurfer_home=os.getenv('FREESURFER_HOME'),
spaces=config.workflow.spaces.get_fs_spaces()),
name='fsdir_run_%s' % config.execution.run_uuid.replace('-', '_'),
run_without_submitting=True)
if config.execution.fs_subjects_dir is not None:
fsdir.inputs.subjects_dir = str(
config.execution.fs_subjects_dir.absolute())
for subject_id in config.execution.participant_label:
single_subject_wf = init_single_subject_wf(subject_id)
single_subject_wf.config['execution']['crashdump_dir'] = str(
config.execution.output_dir / "fmriprep" / "-".join(
("sub", subject_id)) / "log" / config.execution.run_uuid)
for node in single_subject_wf._get_all_nodes():
node.config = deepcopy(single_subject_wf.config)
if freesurfer:
fmriprep_wf.connect(fsdir, 'subjects_dir', single_subject_wf,
'inputnode.subjects_dir')
else:
fmriprep_wf.add_nodes([single_subject_wf])
# Dump a copy of the config file into the log directory
log_dir = config.execution.output_dir / 'fmriprep' / 'sub-{}'.format(subject_id) \
/ 'log' / config.execution.run_uuid
log_dir.mkdir(exist_ok=True, parents=True)
config.to_filename(log_dir / 'fmriprep.toml')
return fmriprep_wf
def init_dmriprep_wf():
"""
Create the base workflow.
This workflow organizes the execution of *dMRIPrep*, 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
from dmriprep.config.testing import mock_config
from dmriprep.workflows.base import init_dmriprep_wf
with mock_config():
wf = init_dmriprep_wf()
"""
dmriprep_wf = Workflow(name="dmriprep_wf")
dmriprep_wf.base_dir = config.execution.work_dir
freesurfer = config.workflow.run_reconall
if freesurfer:
fsdir = pe.Node(
BIDSFreeSurferDir(
derivatives=config.execution.output_dir,
freesurfer_home=os.getenv("FREESURFER_HOME"),
spaces=config.workflow.spaces.get_fs_spaces(),
),
name=f"fsdir_run_{config.execution.run_uuid.replace('-', '_')}",
run_without_submitting=True,
)
if config.execution.fs_subjects_dir is not None:
fsdir.inputs.subjects_dir = str(
config.execution.fs_subjects_dir.absolute())
for subject_id in config.execution.participant_label:
single_subject_wf = init_single_subject_wf(subject_id)
single_subject_wf.config["execution"]["crashdump_dir"] = str(
config.execution.output_dir / "dmriprep" / f"sub-{subject_id}" /
"log" / config.execution.run_uuid)
for node in single_subject_wf._get_all_nodes():
node.config = deepcopy(single_subject_wf.config)
if freesurfer:
dmriprep_wf.connect(fsdir, "subjects_dir", single_subject_wf,
"fsinputnode.subjects_dir")
else:
dmriprep_wf.add_nodes([single_subject_wf])
# Dump a copy of the config file into the log directory
log_dir = (config.execution.output_dir / "dmriprep" /
f"sub-{subject_id}" / "log" / config.execution.run_uuid)
log_dir.mkdir(exist_ok=True, parents=True)
config.to_filename(log_dir / "dmriprep.toml")
return dmriprep_wf
def init_fmriprep_wf(layout, subject_list, task_id, echo_idx, run_uuid,
work_dir, output_dir, ignore, debug, low_mem, anat_only,
longitudinal, t2s_coreg, omp_nthreads,
skull_strip_template, skull_strip_fixed_seed, freesurfer,
output_spaces, template, medial_surface_nan, cifti_output,
hires, use_bbr, bold2t1w_dof, fmap_bspline, fmap_demean,
use_syn, force_syn, use_aroma, err_on_aroma_warn,
aroma_melodic_dim, template_out_grid):
"""
This workflow organizes the execution of FMRIPREP, 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::
:graph2use: orig
:simple_form: yes
import os
from collections import namedtuple
BIDSLayout = namedtuple('BIDSLayout', ['root'], defaults='.')
from fmriprep.workflows.base import init_fmriprep_wf
os.environ['FREESURFER_HOME'] = os.getcwd()
wf = init_fmriprep_wf(layout=BIDSLayout(),
subject_list=['fmripreptest'],
task_id='',
echo_idx=None,
run_uuid='X',
work_dir='.',
output_dir='.',
ignore=[],
debug=False,
low_mem=False,
anat_only=False,
longitudinal=False,
t2s_coreg=False,
omp_nthreads=1,
skull_strip_template='OASIS30ANTs',
skull_strip_fixed_seed=False,
freesurfer=True,
output_spaces=['T1w', 'fsnative',
'template', 'fsaverage5'],
template='MNI152NLin2009cAsym',
medial_surface_nan=False,
cifti_output=False,
hires=True,
use_bbr=True,
bold2t1w_dof=9,
fmap_bspline=False,
fmap_demean=True,
use_syn=True,
force_syn=True,
use_aroma=False,
err_on_aroma_warn=False,
aroma_melodic_dim=-200,
template_out_grid='native')
Parameters
layout : BIDSLayout object
BIDS dataset layout
subject_list : list
List of subject labels
task_id : str or None
Task ID of BOLD series to preprocess, or ``None`` to preprocess all
echo_idx : int or None
Index of echo to preprocess in multiecho BOLD series,
or ``None`` to preprocess all
run_uuid : str
Unique identifier for execution instance
work_dir : str
Directory in which to store workflow execution state and temporary files
output_dir : str
Directory in which to save derivatives
ignore : list
Preprocessing steps to skip (may include "slicetiming", "fieldmaps")
debug : bool
Enable debugging outputs
low_mem : bool
Write uncompressed .nii files in some cases to reduce memory usage
anat_only : bool
Disable functional workflows
longitudinal : bool
Treat multiple sessions as longitudinal (may increase runtime)
See sub-workflows for specific differences
t2s_coreg : bool
For multi-echo EPI, use the calculated T2*-map for T2*-driven coregistration
omp_nthreads : int
Maximum number of threads an individual process may use
skull_strip_template : str
Name of ANTs skull-stripping template ('OASIS30ANTs' or 'NKI')
skull_strip_fixed_seed : bool
Do not use a random seed for skull-stripping - will ensure
run-to-run replicability when used with --omp-nthreads 1
freesurfer : bool
Enable FreeSurfer surface reconstruction (may increase runtime)
output_spaces : list
List of output spaces functional images are to be resampled to.
Some parts of pipeline will only be instantiated for some output spaces.
Valid spaces:
- T1w
- template
- fsnative
- fsaverage (or other pre-existing FreeSurfer templates)
template : str
Name of template targeted by ``template`` output space
medial_surface_nan : bool
Replace medial wall values with NaNs on functional GIFTI files
cifti_output : bool
Generate bold CIFTI file in output spaces
hires : bool
Enable sub-millimeter preprocessing in FreeSurfer
use_bbr : bool or None
Enable/disable boundary-based registration refinement.
If ``None``, test BBR result for distortion before accepting.
bold2t1w_dof : 6, 9 or 12
Degrees-of-freedom for BOLD-T1w registration
fmap_bspline : bool
**Experimental**: Fit B-Spline field using least-squares
fmap_demean : bool
Demean voxel-shift map during unwarp
use_syn : bool
**Experimental**: Enable ANTs SyN-based susceptibility distortion correction (SDC).
If fieldmaps are present and enabled, this is not run, by default.
force_syn : bool
**Temporary**: Always run SyN-based SDC
use_aroma : bool
Perform ICA-AROMA on MNI-resampled functional series
err_on_aroma_warn : bool
Do not fail on ICA-AROMA errors
template_out_grid : str
Keyword ('native', '1mm' or '2mm') or path of custom reference
image for normalization
"""
fmriprep_wf = Workflow(name='fmriprep_wf')
fmriprep_wf.base_dir = work_dir
if freesurfer:
fsdir = pe.Node(BIDSFreeSurferDir(
derivatives=output_dir,
freesurfer_home=os.getenv('FREESURFER_HOME'),
spaces=output_spaces),
name='fsdir_run_' + run_uuid.replace('-', '_'),
run_without_submitting=True)
reportlets_dir = os.path.join(work_dir, 'reportlets')
for subject_id in subject_list:
single_subject_wf = init_single_subject_wf(
layout=layout,
subject_id=subject_id,
task_id=task_id,
echo_idx=echo_idx,
name="single_subject_" + subject_id + "_wf",
reportlets_dir=reportlets_dir,
output_dir=output_dir,
ignore=ignore,
debug=debug,
low_mem=low_mem,
anat_only=anat_only,
longitudinal=longitudinal,
t2s_coreg=t2s_coreg,
omp_nthreads=omp_nthreads,
skull_strip_template=skull_strip_template,
skull_strip_fixed_seed=skull_strip_fixed_seed,
freesurfer=freesurfer,
output_spaces=output_spaces,
template=template,
medial_surface_nan=medial_surface_nan,
cifti_output=cifti_output,
hires=hires,
use_bbr=use_bbr,
bold2t1w_dof=bold2t1w_dof,
fmap_bspline=fmap_bspline,
fmap_demean=fmap_demean,
use_syn=use_syn,
force_syn=force_syn,
template_out_grid=template_out_grid,
use_aroma=use_aroma,
aroma_melodic_dim=aroma_melodic_dim,
err_on_aroma_warn=err_on_aroma_warn,
)
single_subject_wf.config['execution']['crashdump_dir'] = (os.path.join(
output_dir, "fmriprep", "sub-" + subject_id, 'log', run_uuid))
for node in single_subject_wf._get_all_nodes():
node.config = deepcopy(single_subject_wf.config)
if freesurfer:
fmriprep_wf.connect(fsdir, 'subjects_dir', single_subject_wf,
'inputnode.subjects_dir')
else:
fmriprep_wf.add_nodes([single_subject_wf])
return fmriprep_wf
def init_smriprep_wf(
debug,
fast_track,
freesurfer,
fs_subjects_dir,
hires,
layout,
longitudinal,
low_mem,
omp_nthreads,
output_dir,
run_uuid,
skull_strip_mode,
skull_strip_fixed_seed,
skull_strip_template,
spaces,
subject_list,
work_dir,
bids_filters,
):
"""
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
wf = init_smriprep_wf(
debug=False,
fast_track=False,
freesurfer=True,
fs_subjects_dir=None,
hires=True,
layout=BIDSLayout('.'),
longitudinal=False,
low_mem=False,
omp_nthreads=1,
output_dir='.',
run_uuid='testrun',
skull_strip_fixed_seed=False,
skull_strip_mode='force',
skull_strip_template=Reference('OASIS30ANTs'),
spaces=SpatialReferences(spaces=['MNI152NLin2009cAsym', 'fsaverage5']),
subject_list=['smripreptest'],
work_dir='.',
bids_filters=None,
)
Parameters
----------
debug : :obj:`bool`
Enable debugging outputs
fast_track : :obj:`bool`
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
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(
debug=debug,
freesurfer=freesurfer,
fast_track=fast_track,
hires=hires,
layout=layout,
longitudinal=longitudinal,
low_mem=low_mem,
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,
)
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
def init_fmriprep_wf(
anat_only,
aroma_melodic_dim,
bold2t1w_dof,
cifti_output,
debug,
dummy_scans,
echo_idx,
err_on_aroma_warn,
fmap_bspline,
fmap_demean,
force_syn,
freesurfer,
fs_subjects_dir,
hires,
ignore,
layout,
longitudinal,
low_mem,
medial_surface_nan,
omp_nthreads,
output_dir,
regressors_all_comps,
regressors_dvars_th,
regressors_fd_th,
run_uuid,
skull_strip_fixed_seed,
skull_strip_template,
spaces,
subject_list,
t2s_coreg,
task_id,
use_aroma,
use_bbr,
use_syn,
work_dir,
):
"""
Build *fMRIPrep*'s pipeline.
This workflow organizes the execution of FMRIPREP, with a sub-workflow for
each subject.
If FreeSurfer's ``recon-all`` is to be run, a corresponding folder is created
and populated with any needed template subjects under the derivatives folder.
Workflow Graph
.. workflow::
:graph2use: orig
:simple_form: yes
import os
from collections import namedtuple, OrderedDict
BIDSLayout = namedtuple('BIDSLayout', ['root'])
from fmriprep.workflows.base import init_fmriprep_wf
from niworkflows.utils.spaces import Reference, SpatialReferences
os.environ['FREESURFER_HOME'] = os.getcwd()
wf = init_fmriprep_wf(
anat_only=False,
aroma_melodic_dim=-200,
bold2t1w_dof=9,
cifti_output=False,
debug=False,
dummy_scans=None,
echo_idx=None,
err_on_aroma_warn=False,
fmap_bspline=False,
fmap_demean=True,
force_syn=True,
freesurfer=True,
fs_subjects_dir=None,
hires=True,
ignore=[],
layout=BIDSLayout('.'),
longitudinal=False,
low_mem=False,
medial_surface_nan=False,
omp_nthreads=1,
output_dir='.',
regressors_all_comps=False,
regressors_dvars_th=1.5,
regressors_fd_th=0.5,
run_uuid='X',
skull_strip_fixed_seed=False,
skull_strip_template=Reference('OASIS30ANTs'),
spaces=SpatialReferences(
spaces=['MNI152Lin',
('fsaverage', {'density': '10k'}),
'T1w',
'fsnative'],
checkpoint=True),
subject_list=['fmripreptest'],
t2s_coreg=False,
task_id='',
use_aroma=False,
use_bbr=True,
use_syn=True,
work_dir='.',
)
Parameters
----------
anat_only : bool
Disable functional workflows
bold2t1w_dof : 6, 9 or 12
Degrees-of-freedom for BOLD-T1w registration
cifti_output : bool
Generate bold CIFTI file in output spaces
debug : bool
Enable debugging outputs
dummy_scans : int or None
Number of volumes to consider as non steady state
echo_idx : int or None
Index of echo to preprocess in multiecho BOLD series,
or ``None`` to preprocess all
err_on_aroma_warn : bool
Do not fail on ICA-AROMA errors
fmap_bspline : bool
**Experimental**: Fit B-Spline field using least-squares
fmap_demean : bool
Demean voxel-shift map during unwarp
force_syn : bool
**Temporary**: Always run SyN-based SDC
freesurfer : bool
Enable FreeSurfer surface reconstruction (may increase runtime)
hires : bool
Enable sub-millimeter preprocessing in FreeSurfer
ignore : list
Preprocessing steps to skip (may include "slicetiming", "fieldmaps")
layout : BIDSLayout object
BIDS dataset layout
longitudinal : bool
Treat multiple sessions as longitudinal (may increase runtime)
See sub-workflows for specific differences
low_mem : bool
Write uncompressed .nii files in some cases to reduce memory usage
medial_surface_nan : bool
Replace medial wall values with NaNs on functional GIFTI files
omp_nthreads : int
Maximum number of threads an individual process may use
output_dir : str
Directory in which to save derivatives
regressors_all_comps
Return all CompCor component time series instead of the top fraction
regressors_dvars_th
Criterion for flagging DVARS outliers
regressors_fd_th
Criterion for flagging framewise displacement outliers
run_uuid : str
Unique identifier for execution instance
skull_strip_template : tuple
Name of target template for brain extraction with ANTs' ``antsBrainExtraction``,
and corresponding dictionary of output-space modifiers.
skull_strip_fixed_seed : bool
Do not use a random seed for skull-stripping - will ensure
run-to-run replicability when used with --omp-nthreads 1
spaces : :py:class:`~niworkflows.utils.spaces.SpatialReferences`
A container for storing, organizing, and parsing spatial normalizations. Composed of
:py:class:`~niworkflows.utils.spaces.Reference` objects representing spatial references.
Each ``Reference`` contains a space, which is a string of either TemplateFlow template IDs
(e.g., ``MNI152Lin``, ``MNI152NLin6Asym``, ``MNIPediatricAsym``), nonstandard references
(e.g., ``T1w`` or ``anat``, ``sbref``, ``run``, etc.), or a custom template located in
the TemplateFlow root directory. Each ``Reference`` may also contain a spec, which is a
dictionary with template specifications (e.g., a specification of ``{'resolution': 2}``
would lead to resampling on a 2mm resolution of the space).
subject_list : list
List of subject labels
t2s_coreg : bool
For multi-echo EPI, use the calculated T2*-map for T2*-driven coregistration
task_id : str or None
Task ID of BOLD series to preprocess, or ``None`` to preprocess all
use_aroma : bool
Perform ICA-AROMA on MNI-resampled functional series
use_bbr : bool or None
Enable/disable boundary-based registration refinement.
If ``None``, test BBR result for distortion before accepting.
use_syn : bool
**Experimental**: Enable ANTs SyN-based susceptibility distortion correction (SDC).
If fieldmaps are present and enabled, this is not run, by default.
work_dir : str
Directory in which to store workflow execution state and temporary files
"""
fmriprep_wf = Workflow(name='fmriprep_wf')
fmriprep_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_' + run_uuid.replace('-', '_'), run_without_submitting=True)
if fs_subjects_dir is not None:
fsdir.inputs.subjects_dir = str(fs_subjects_dir.absolute())
reportlets_dir = os.path.join(work_dir, 'reportlets')
for subject_id in subject_list:
single_subject_wf = init_single_subject_wf(
anat_only=anat_only,
aroma_melodic_dim=aroma_melodic_dim,
bold2t1w_dof=bold2t1w_dof,
cifti_output=cifti_output,
debug=debug,
dummy_scans=dummy_scans,
echo_idx=echo_idx,
err_on_aroma_warn=err_on_aroma_warn,
fmap_bspline=fmap_bspline,
fmap_demean=fmap_demean,
force_syn=force_syn,
freesurfer=freesurfer,
hires=hires,
ignore=ignore,
layout=layout,
longitudinal=longitudinal,
low_mem=low_mem,
medial_surface_nan=medial_surface_nan,
name="single_subject_" + subject_id + "_wf",
omp_nthreads=omp_nthreads,
output_dir=output_dir,
regressors_all_comps=regressors_all_comps,
regressors_dvars_th=regressors_dvars_th,
regressors_fd_th=regressors_fd_th,
reportlets_dir=reportlets_dir,
skull_strip_fixed_seed=skull_strip_fixed_seed,
skull_strip_template=skull_strip_template,
spaces=spaces,
subject_id=subject_id,
t2s_coreg=t2s_coreg,
task_id=task_id,
use_aroma=use_aroma,
use_bbr=use_bbr,
use_syn=use_syn,
)
single_subject_wf.config['execution']['crashdump_dir'] = (
os.path.join(output_dir, "fmriprep", "sub-" + subject_id, 'log', run_uuid)
)
for node in single_subject_wf._get_all_nodes():
node.config = deepcopy(single_subject_wf.config)
if freesurfer:
fmriprep_wf.connect(fsdir, 'subjects_dir',
single_subject_wf, 'inputnode.subjects_dir')
else:
fmriprep_wf.add_nodes([single_subject_wf])
return fmriprep_wf
def init_dmriprep_wf(
anat_only,
debug,
force_syn,
freesurfer,
hires,
ignore,
layout,
longitudinal,
low_mem,
omp_nthreads,
output_dir,
output_spaces,
run_uuid,
skull_strip_fixed_seed,
skull_strip_template,
subject_list,
use_syn,
work_dir,
):
"""
Create the base workflow.
This workflow organizes the execution of *dMRIPrep*, 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, OrderedDict
BIDSLayout = namedtuple('BIDSLayout', ['root'])
from dmriprep.workflows.base import init_dmriprep_wf
os.environ['FREESURFER_HOME'] = os.getcwd()
wf = init_dmriprep_wf(
anat_only=False,
debug=False,
force_syn=True,
freesurfer=True,
hires=True,
ignore=[],
layout=BIDSLayout('.'),
longitudinal=False,
low_mem=False,
omp_nthreads=1,
output_dir='.',
output_spaces=OrderedDict([
('MNI152Lin', {}), ('fsaverage', {'density': '10k'}),
('T1w', {}), ('fsnative', {})]),
run_uuid='X',
skull_strip_fixed_seed=False,
skull_strip_template=('OASIS30ANTs', {}),
subject_list=['dmripreptest'],
use_syn=True,
work_dir='.',
)
Parameters
----------
anat_only : bool
Disable diffusion MRI workflows
debug : bool
Enable debugging outputs
force_syn : bool
**Temporary**: Always run SyN-based SDC
freesurfer : bool
Enable FreeSurfer surface reconstruction (may increase runtime)
hires : bool
Enable sub-millimeter preprocessing in FreeSurfer
ignore : list
Preprocessing steps to skip (may include "slicetiming", "fieldmaps")
layout : BIDSLayout object
BIDS dataset layout
longitudinal : bool
Treat multiple sessions as longitudinal (may increase runtime)
See sub-workflows for specific differences
low_mem : bool
Write uncompressed .nii files in some cases to reduce memory usage
omp_nthreads : int
Maximum number of threads an individual process may use
output_dir : str
Directory in which to save derivatives
output_spaces : OrderedDict
Ordered dictionary where keys are TemplateFlow ID strings (e.g., ``MNI152Lin``,
``MNI152NLin6Asym``, ``MNI152NLin2009cAsym``, or ``fsLR``) strings designating
nonstandard references (e.g., ``T1w`` or ``anat``, ``sbref``, ``run``, etc.),
or paths pointing to custom templates organized in a TemplateFlow-like structure.
Values of the dictionary aggregate modifiers (e.g., the value for the key ``MNI152Lin``
could be ``{'resolution': 2}`` if one wants the resampling to be done on the 2mm
resolution version of the selected template).
run_uuid : str
Unique identifier for execution instance
skull_strip_template : tuple
Name of target template for brain extraction with ANTs' ``antsBrainExtraction``,
and corresponding dictionary of output-space modifiers.
skull_strip_fixed_seed : bool
Do not use a random seed for skull-stripping - will ensure
run-to-run replicability when used with --omp-nthreads 1
subject_list : list
List of subject labels
use_syn : bool
**Experimental**: Enable ANTs SyN-based susceptibility distortion correction (SDC).
If fieldmaps are present and enabled, this is not run, by default.
work_dir : str
Directory in which to store workflow execution state and temporary files
"""
dmriprep_wf = Workflow(name='dmriprep_wf')
dmriprep_wf.base_dir = work_dir
if freesurfer:
fsdir = pe.Node(BIDSFreeSurferDir(
derivatives=output_dir,
freesurfer_home=os.getenv('FREESURFER_HOME'),
spaces=[
s for s in output_spaces.keys() if s.startswith('fsaverage')
] + ['fsnative'] * ('fsnative' in output_spaces)),
name='fsdir_run_' + run_uuid.replace('-', '_'),
run_without_submitting=True)
reportlets_dir = os.path.join(work_dir, 'reportlets')
for subject_id in subject_list:
single_subject_wf = init_single_subject_wf(
anat_only=anat_only,
debug=debug,
force_syn=force_syn,
freesurfer=freesurfer,
hires=hires,
ignore=ignore,
layout=layout,
longitudinal=longitudinal,
low_mem=low_mem,
name="single_subject_" + subject_id + "_wf",
omp_nthreads=omp_nthreads,
output_dir=output_dir,
output_spaces=output_spaces,
reportlets_dir=reportlets_dir,
skull_strip_fixed_seed=skull_strip_fixed_seed,
skull_strip_template=skull_strip_template,
subject_id=subject_id,
use_syn=use_syn,
)
single_subject_wf.config['execution']['crashdump_dir'] = (os.path.join(
output_dir, "dmriprep", "sub-" + subject_id, 'log', run_uuid))
for node in single_subject_wf._get_all_nodes():
node.config = deepcopy(single_subject_wf.config)
if freesurfer:
dmriprep_wf.connect(fsdir, 'subjects_dir', single_subject_wf,
'inputnode.subjects_dir')
else:
dmriprep_wf.add_nodes([single_subject_wf])
return dmriprep_wf
def init_smriprep_wf(
debug,
freesurfer,
hires,
layout,
longitudinal,
low_mem,
omp_nthreads,
output_dir,
output_spaces,
run_uuid,
skull_strip_fixed_seed,
skull_strip_template,
subject_list,
work_dir,
):
"""
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::
:graph2use: orig
:simple_form: yes
import os
from collections import OrderedDict, namedtuple
BIDSLayout = namedtuple('BIDSLayout', ['root'])
os.environ['FREESURFER_HOME'] = os.getcwd()
from smriprep.workflows.base import init_smriprep_wf
wf = init_smriprep_wf(
debug=False,
freesurfer=True,
hires=True,
layout=BIDSLayout('.'),
longitudinal=False,
low_mem=False,
omp_nthreads=1,
output_dir='.',
output_spaces=OrderedDict([('MNI152NLin2009cAsym', {}),
('fsaverage5', {})]),
run_uuid='testrun',
skull_strip_fixed_seed=False,
skull_strip_template=('OASIS30ANTs', {}),
subject_list=['smripreptest'],
work_dir='.',
)
**Parameters**
debug : bool
Enable debugging outputs
freesurfer : bool
Enable FreeSurfer surface reconstruction (may increase runtime)
hires : bool
Enable sub-millimeter preprocessing in FreeSurfer
layout : BIDSLayout object
BIDS dataset layout
longitudinal : bool
Treat multiple sessions as longitudinal (may increase runtime)
See sub-workflows for specific differences
low_mem : bool
Write uncompressed .nii files in some cases to reduce memory usage
omp_nthreads : int
Maximum number of threads an individual process may use
output_dir : str
Directory in which to save derivatives
output_spaces : OrderedDict
List of spatial normalization targets. Some parts of pipeline will
only be instantiated for some output spaces. Valid spaces:
- Any template identifier from TemplateFlow
- Path to a template folder organized following TemplateFlow's
conventions
run_uuid : str
Unique identifier for execution instance
skull_strip_fixed_seed : bool
Do not use a random seed for skull-stripping - will ensure
run-to-run replicability when used with --omp-nthreads 1
skull_strip_template : tuple
Name of ANTs skull-stripping template ('OASIS30ANTs' or 'NKI'),
and dictionary with template specifications (e.g., {'res': '2'})
subject_list : list
List of subject labels
work_dir : str
Directory in which to store workflow execution state and
temporary files
"""
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=[
s for s in output_spaces.keys() if s.startswith('fsaverage')
] + ['fsnative'] * ('fsnative' in output_spaces)),
name='fsdir_run_%s' % run_uuid.replace('-', '_'),
run_without_submitting=True)
reportlets_dir = os.path.join(work_dir, 'reportlets')
for subject_id in subject_list:
single_subject_wf = init_single_subject_wf(
debug=debug,
freesurfer=freesurfer,
hires=hires,
layout=layout,
longitudinal=longitudinal,
low_mem=low_mem,
name="single_subject_%s_wf" % subject_id,
omp_nthreads=omp_nthreads,
output_dir=output_dir,
output_spaces=output_spaces,
reportlets_dir=reportlets_dir,
skull_strip_fixed_seed=skull_strip_fixed_seed,
skull_strip_template=skull_strip_template,
subject_id=subject_id,
)
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
def init_nibabies_wf():
"""
Build *NiBabies*'s pipeline.
This workflow organizes the execution of NiBabies, with a sub-workflow for
each subject.
If FreeSurfer's ``infant_recon_all`` is to be run, a corresponding folder is created
and populated with any needed template subjects under the derivatives folder.
Workflow Graph
.. workflow::
:graph2use: orig
:simple_form: yes
from nibabies.workflows.tests import mock_config
from nibabies.workflows.base import init_nibabies_wf
with mock_config():
wf = init_nibabies_wf()
"""
from niworkflows.engine.workflows import LiterateWorkflow as Workflow
from niworkflows.interfaces.bids import BIDSFreeSurferDir
nibabies_wf = Workflow(name="nibabies_wf")
nibabies_wf.base_dir = config.execution.work_dir
freesurfer = config.workflow.run_reconall
if freesurfer:
fsdir = pe.Node(
BIDSFreeSurferDir(
derivatives=config.execution.output_dir,
freesurfer_home=os.getenv("FREESURFER_HOME"),
spaces=config.workflow.spaces.get_fs_spaces(),
),
name=f"fsdir_run_{config.execution.run_uuid.replace('-', '_')}",
run_without_submitting=True,
)
if config.execution.fs_subjects_dir is not None:
fsdir.inputs.subjects_dir = str(
config.execution.fs_subjects_dir.absolute())
for subject_id in config.execution.participant_label:
single_subject_wf = init_single_subject_wf(subject_id)
single_subject_wf.config["execution"]["crashdump_dir"] = str(
config.execution.fmriprep_dir / f"sub-{subject_id}" / "log" /
config.execution.run_uuid)
for node in single_subject_wf._get_all_nodes():
node.config = deepcopy(single_subject_wf.config)
if freesurfer:
nibabies_wf.connect(fsdir, "subjects_dir", single_subject_wf,
"inputnode.subjects_dir")
else:
nibabies_wf.add_nodes([single_subject_wf])
# Dump a copy of the config file into the log directory
log_dir = (config.execution.fmriprep_dir / f"sub-{subject_id}" /
"log" / config.execution.run_uuid)
log_dir.mkdir(exist_ok=True, parents=True)
config.to_filename(log_dir / "nibabies.toml")
return nibabies_wf