fix: Report pre-computed bold2t1w registration

Author: effigies

fmriprep/interfaces/reports.py

@@ -204,7 +204,11 @@ class FunctionalSummaryInputSpec(TraitedSpec):
         desc='Phase-encoding direction detected',
     )
     registration = traits.Enum(
-        'FSL', 'FreeSurfer', mandatory=True, desc='Functional/anatomical registration method'
+        'FSL',
+        'FreeSurfer',
+        'Precomputed',
+        mandatory=True,
+        desc='Functional/anatomical registration method',
     )
     fallback = traits.Bool(desc='Boundary-based registration rejected')
     registration_dof = traits.Enum(
@@ -239,18 +243,21 @@ def _generate_segment(self):
         else:
             stc = 'n/a'
         # TODO: Add a note about registration_init below?
-        reg = {
-            'FSL': [
-                'FSL <code>flirt</code> with boundary-based registration'
-                f' (BBR) metric - {dof} dof',
-                'FSL <code>flirt</code> rigid registration - 6 dof',
-            ],
-            'FreeSurfer': [
-                'FreeSurfer <code>bbregister</code> '
-                f'(boundary-based registration, BBR) - {dof} dof',
-                f'FreeSurfer <code>mri_coreg</code> - {dof} dof',
-            ],
-        }[self.inputs.registration][self.inputs.fallback]
+        if self.inputs.registration == 'Precomputed':
+            reg = 'Precomputed affine transformation'
+        else:
+            reg = {
+                'FSL': [
+                    'FSL <code>flirt</code> with boundary-based registration'
+                    f' (BBR) metric - {dof} dof',
+                    'FSL <code>flirt</code> rigid registration - 6 dof',
+                ],
+                'FreeSurfer': [
+                    'FreeSurfer <code>bbregister</code> '
+                    f'(boundary-based registration, BBR) - {dof} dof',
+                    f'FreeSurfer <code>mri_coreg</code> - {dof} dof',
+                ],
+            }[self.inputs.registration][self.inputs.fallback]
 
         pedir = get_world_pedir(self.inputs.orientation, self.inputs.pe_direction)
 

fmriprep/workflows/bold/fit.py

@@ -307,7 +307,13 @@ def init_bold_fit_wf(
     summary = pe.Node(
         FunctionalSummary(
             distortion_correction='None',  # Can override with connection
-            registration=('FSL', 'FreeSurfer')[config.workflow.run_reconall],
+            registration=(
+                'Precomputed'
+                if boldref2anat_xform
+                else 'FreeSurfer'
+                if config.workflow.run_reconall
+                else 'FSL'
+            ),
             registration_dof=config.workflow.bold2anat_dof,
             registration_init=config.workflow.bold2anat_init,
             pe_direction=metadata.get('PhaseEncodingDirection'),