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fix collect freesurfer #3588

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fix collect freesurfer #3588

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10 changes: 6 additions & 4 deletions fmriprep/workflows/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -397,10 +397,7 @@ def init_single_subject_wf(
]),
(bidssrc, src_file, [('out_dict', 'bids_info')]),
(src_file, bids_info, [('source_file', 'in_file')]),
(bids_info, create_fs_id, [
('subject', 'subject_id'),
('session', 'session_id'),
]),
(bids_info, create_fs_id, [('subject', 'subject_id')]),
(create_fs_id, anat_fit_wf, [('subject_id', 'inputnode.subject_id')]),
# Reporting connections
(inputnode, summary, [('subjects_dir', 'subjects_dir')]),
Expand All @@ -410,6 +407,11 @@ def init_single_subject_wf(
(about, ds_report_about, [('out_report', 'in_file')]),
]) # fmt:skip

if config.workflow.subject_anatomical_reference == 'sessionwise':
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@tsalo tsalo Dec 16, 2025

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What about something like this?

Suggested change
if config.workflow.subject_anatomical_reference == 'sessionwise':
if (config.workflow.subject_anatomical_reference == 'sessionwise') or (config.workflow.session_label is not None):

workflow.connect([
(bids_info, create_fs_id, [('session', 'session_id')]),
]) # fmt:skip

# Set up the template iterator once, if used
template_iterator_wf = None
select_MNI2009c_xfm = None
Expand Down