Merge tag '0.19.2'

0.19.2 (September 24, 2025)

Bug-fix release in the 0.19.x series.

For users attempting to run sMRIPrep or fMRIPrep with precomputed derivatives,
the FreeSurfer-to-anat transform was being found but not passed to the relevant nodes.
This should only affect users who deleted subject-native surface GIFTI files in an
effort to save space.

This fix does not change the calculation of the transform, so users do not need to
recalculate the transform to benefit from this fix.

* FIX: Use pre-computed FreeSurfer-to-anat transform, when found (#497)

Author: effigies

CHANGES.rst

@@ -1,3 +1,17 @@
+0.19.2 (September 24, 2025)
+===========================
+Bug-fix release in the 0.19.x series.
+
+For users attempting to run sMRIPrep or fMRIPrep with precomputed derivatives,
+the FreeSurfer-to-anat transform was being found but not passed to the relevant nodes.
+This should only affect users who deleted subject-native surface GIFTI files in an
+effort to save space.
+
+This fix does not change the calculation of the transform, so users do not need to
+recalculate the transform to benefit from this fix.
+
+* FIX: Use pre-computed FreeSurfer-to-anat transform, when found (#497)
+
 0.19.1 (September 12, 2025)
 ===========================
 Bug-fix release in the 0.19.x series.

src/smriprep/workflows/anatomical.py

@@ -707,6 +707,11 @@ def init_anat_fit_wf(
     anat2std_buffer = pe.Node(niu.Merge(2), name='anat2std_buffer')
     std2anat_buffer = pe.Node(niu.Merge(2), name='std2anat_buffer')
 
+    # Stage 5 results: FreeSurfer-to-anat transforms
+    fs2anat_buffer = pe.Node(
+        niu.IdentityInterface(fields=['fsnative2anat_xfm']), name='fs2anat_buffer'
+    )
+
     # Stage 6 results: Refined stage 2 results; may be direct copy if no refinement
     refined_buffer = pe.Node(
         niu.IdentityInterface(fields=['t1w_mask', 't1w_brain']),
@@ -733,6 +738,7 @@ def init_anat_fit_wf(
         (anat2std_buffer, outputnode, [('out', 'anat2std_xfm')]),
         (std2anat_buffer, outputnode, [('out', 'std2anat_xfm')]),
         (template_buffer, outputnode, [('out', 'template')]),
+        (fs2anat_buffer, outputnode, [('fsnative2anat_xfm', 'fsnative2t1w_xfm')]),
         (sourcefile_buffer, outputnode, [('source_files', 't1w_valid_list')]),
         (surfaces_buffer, outputnode, [
             ('white', 'white'),
@@ -1089,13 +1095,13 @@ def init_anat_fit_wf(
             (surface_recon_wf, ds_fs_registration_wf, [
                 ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2anat_xfm'),
             ]),
-            (ds_fs_registration_wf, outputnode, [
-                ('outputnode.fsnative2anat_xfm', 'fsnative2t1w_xfm'),
+            (ds_fs_registration_wf, fs2anat_buffer, [
+                ('outputnode.fsnative2anat_xfm', 'fsnative2anat_xfm'),
             ]),
         ])  # fmt:skip
     elif 'reverse' in fsnative_xfms:
         LOGGER.info('ANAT Found fsnative-T1w transform - skipping registration')
-        outputnode.inputs.fsnative2t1w_xfm = fsnative_xfms['reverse']
+        fs2anat_buffer.inputs.fsnative2anat_xfm = fsnative_xfms['reverse']
     else:
         raise RuntimeError(
             'Found a T1w-to-fsnative transform without the reverse. Time to handle this.'
@@ -1111,12 +1117,14 @@ def init_anat_fit_wf(
             (surface_recon_wf, refinement_wf, [
                 ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
                 ('outputnode.subject_id', 'inputnode.subject_id'),
-                ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2anat_xfm'),
             ]),
             (t1w_buffer, refinement_wf, [
                 ('t1w_preproc', 'inputnode.reference_image'),
                 ('ants_seg', 'inputnode.ants_segs'),
             ]),
+            (fs2anat_buffer, refinement_wf, [
+                ('fsnative2anat_xfm', 'inputnode.fsnative2anat_xfm'),
+            ]),
             (t1w_buffer, applyrefined, [('t1w_preproc', 'in_file')]),
             (refinement_wf, applyrefined, [('outputnode.out_brainmask', 'mask_file')]),
             (refinement_wf, refined_buffer, [('outputnode.out_brainmask', 't1w_mask')]),
@@ -1171,7 +1179,7 @@ def init_anat_fit_wf(
                 ('outputnode.subjects_dir', 'subjects_dir'),
             ]),
             (bbreg, coreg_xfms, [('out_lta_file', 'in1')]),
-            (surface_recon_wf, coreg_xfms, [('outputnode.fsnative2t1w_xfm', 'in2')]),
+            (fs2anat_buffer, coreg_xfms, [('fsnative2anat_xfm', 'in2')]),
             (coreg_xfms, t2wtot1w_xfm, [('out', 'in_xfms')]),
             (t2w_template_wf, t2w_resample, [('outputnode.anat_ref', 'input_image')]),
             (t1w_buffer, t2w_resample, [('t1w_preproc', 'reference_image')]),
@@ -1217,7 +1225,9 @@ def init_anat_fit_wf(
             (surface_recon_wf, gifti_surfaces_wf, [
                 ('outputnode.subject_id', 'inputnode.subject_id'),
                 ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
-                ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2anat_xfm'),
+            ]),
+            (fs2anat_buffer, gifti_surfaces_wf, [
+                ('fsnative2anat_xfm', 'inputnode.fsnative2anat_xfm'),
             ]),
             (sourcefile_buffer, ds_surfaces_wf, [('source_files', 'inputnode.source_files')]),
             (gifti_surfaces_wf, ds_surfaces_wf, [