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Support session-wise anatomical processing #479

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Support session-wise anatomical processing #479

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df7237c
Add session_id parameter to collect_derivatives.
tsalo Mar 29, 2024
5e66cff
Merge remote-tracking branch 'upstream/master' into longitudinal-deri…
tsalo May 6, 2025
ab6ace0
Update base.py
tsalo May 6, 2025
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18 changes: 17 additions & 1 deletion src/smriprep/utils/bids.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,14 @@
import smriprep


def collect_derivatives(derivatives_dir, subject_id, std_spaces, spec=None, patterns=None):
def collect_derivatives(
derivatives_dir,
subject_id,
std_spaces,
spec=None,
patterns=None,
session_id=None,
):
"""Gather existing derivatives and compose a cache."""
if spec is None or patterns is None:
_spec, _patterns = tuple(loads(smriprep.load_data('io_spec.json').read_text()).values())
Expand All @@ -47,6 +54,9 @@ def collect_derivatives(derivatives_dir, subject_id, std_spaces, spec=None, patt
derivs_cache = {}
for key, qry in spec['baseline'].items():
qry['subject'] = subject_id
if session_id:
qry['session'] = session_id

item = layout.get(return_type='filename', **qry)
if not item:
continue
Expand All @@ -59,6 +69,9 @@ def collect_derivatives(derivatives_dir, subject_id, std_spaces, spec=None, patt
for key, qry in spec['transforms'].items():
qry = qry.copy()
qry['subject'] = subject_id
if session_id:
qry['session'] = session_id

qry['from'] = qry['from'] or space
qry['to'] = qry['to'] or space
item = layout.get(return_type='filename', **qry)
Expand All @@ -68,6 +81,9 @@ def collect_derivatives(derivatives_dir, subject_id, std_spaces, spec=None, patt

for key, qry in spec['surfaces'].items():
qry['subject'] = subject_id
if session_id:
qry['session'] = session_id

item = layout.get(return_type='filename', **qry)
if not item or len(item) != 2:
continue
Expand Down
46 changes: 34 additions & 12 deletions src/smriprep/workflows/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ def init_smriprep_wf(
skull_strip_fixed_seed,
skull_strip_template,
spaces,
subject_list,
subworkflows_list,
work_dir,
bids_filters,
cifti_output,
Expand Down Expand Up @@ -102,7 +102,7 @@ def init_smriprep_wf(
skull_strip_mode='force',
skull_strip_template=Reference('OASIS30ANTs'),
spaces=spaces,
subject_list=['smripreptest'],
subworkflows_list=[('smripreptest', None)],
work_dir='.',
bids_filters=None,
cifti_output=None,
Expand Down Expand Up @@ -148,8 +148,8 @@ def init_smriprep_wf(
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
subworkflows_list : :obj:`list` of :obj:`tuple`
List of subject-session label pairs
work_dir : :obj:`str`
Directory in which to store workflow execution state and
temporary files
Expand All @@ -174,7 +174,17 @@ def init_smriprep_wf(
if fs_subjects_dir is not None:
fsdir.inputs.subjects_dir = str(fs_subjects_dir.absolute())

for subject_id in subject_list:
for subject_id, session_ids in subworkflows_list:
ses_str = session_ids
if not isinstance(session_ids, (str, type(None))):
ses_str = '_'.join(session_ids)

name = (
f'single_subject_{subject_id}_{ses_str}_wf'
if session_ids
else f'single_subject_{subject_id}_wf'
)

single_subject_wf = init_single_subject_wf(
sloppy=sloppy,
debug=debug,
Expand All @@ -186,14 +196,15 @@ def init_smriprep_wf(
longitudinal=longitudinal,
low_mem=low_mem,
msm_sulc=msm_sulc,
name=f'single_subject_{subject_id}_wf',
name=name,
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,
session_id=session_ids,
bids_filters=bids_filters,
cifti_output=cifti_output,
)
Expand Down Expand Up @@ -231,6 +242,7 @@ def init_single_subject_wf(
skull_strip_template,
spaces,
subject_id,
session_id,
bids_filters,
cifti_output,
):
Expand All @@ -241,8 +253,8 @@ def init_single_subject_wf(
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.
Anatomical preprocessing is typically performed in a single workflow,
regardless of the number of sessions, unless the session_id parameter is provided.
Functional preprocessing is performed using a separate workflow for each
individual BOLD series.

Expand Down Expand Up @@ -276,6 +288,7 @@ def init_single_subject_wf(
skull_strip_template=Reference('OASIS30ANTs'),
spaces=spaces,
subject_id='test',
session_id=None,
bids_filters=None,
cifti_output=None,
)
Expand Down Expand Up @@ -320,7 +333,9 @@ def init_single_subject_wf(
spaces : :py:class:`~niworkflows.utils.spaces.SpatialReferences`
Object containing standard and nonstandard space specifications.
subject_id : :obj:`str`
List of subject labels
Subject label
session_id : :obj:`str` or None
Session label
bids_filters : dict
Provides finer specification of the pipeline input files through pybids entities filters.
A dict with the following structure {<suffix>:{<entity>:<filter>,...},...}
Expand Down Expand Up @@ -375,7 +390,9 @@ def init_single_subject_wf(
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))
deriv_cache.update(
collect_derivatives(deriv_dir, subject_id, std_spaces, session_id=session_id)
)

inputnode = pe.Node(niu.IdentityInterface(fields=['subjects_dir']), name='inputnode')

Expand All @@ -397,10 +414,15 @@ def init_single_subject_wf(
run_without_submitting=True,
)

if session_id is not None:
dismiss_entities = None
else:
dismiss_entities = ('session',)

ds_report_summary = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
dismiss_entities=('session',),
dismiss_entities=dismiss_entities,
desc='summary',
datatype='figures',
),
Expand All @@ -411,7 +433,7 @@ def init_single_subject_wf(
ds_report_about = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
dismiss_entities=('session',),
dismiss_entities=dismiss_entities,
desc='about',
datatype='figures',
),
Expand Down
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