ENH: Add --fs-subjects-dir flag

Author: effigies

fmriprep/cli/run.py

@@ -249,6 +249,10 @@ def get_parser():
         '--fs-license-file', metavar='PATH', type=Path,
         help='Path to FreeSurfer license key file. Get it (for free) by registering'
              ' at https://surfer.nmr.mgh.harvard.edu/registration.html')
+    g_fs.add_argument(
+        '--fs-subjects-dir', metavar='PATH', type=Path,
+        help='Path to existing FreeSurfer subjects directory to reuse. '
+             '(default: OUTPUT_DIR/freesurfer)')
 
     # Surface generation xor
     g_surfs = parser.add_argument_group('Surface preprocessing options')
@@ -673,6 +677,7 @@ def build_workflow(opts, retval):
         fmap_demean=opts.fmap_no_demean,
         force_syn=opts.force_syn,
         freesurfer=opts.run_reconall,
+        fs_subjects_dir=opts.fs_subjects_dir,
         hires=opts.hires,
         ignore=opts.ignore,
         layout=layout,

fmriprep/workflows/base.py

@@ -47,6 +47,7 @@ def init_fmriprep_wf(
     fmap_demean,
     force_syn,
     freesurfer,
+    fs_subjects_dir,
     hires,
     ignore,
     layout,
@@ -101,6 +102,7 @@ def init_fmriprep_wf(
                 fmap_demean=True,
                 force_syn=True,
                 freesurfer=True,
+                fs_subjects_dir=None,
                 hires=True,
                 ignore=[],
                 layout=BIDSLayout('.'),
@@ -221,6 +223,8 @@ def init_fmriprep_wf(
                 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)
+        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: