feat: Create GeneratedBy metadata for xfm files

Author: effigies

fmriprep/workflows/bold/fit.py

@@ -682,7 +682,10 @@ def init_bold_fit_wf(
             (regref_buffer, bold_reg_wf, [('boldref', 'inputnode.ref_bold_brain')]),
             # Incomplete sources
             (regref_buffer, ds_boldreg_wf, [('boldref', 'inputnode.source_files')]),
-            (bold_reg_wf, ds_boldreg_wf, [('outputnode.itk_bold_to_t1', 'inputnode.xform')]),
+            (bold_reg_wf, ds_boldreg_wf, [
+                ('outputnode.itk_bold_to_t1', 'inputnode.xform'),
+                ('outputnode.metadata', 'inputnode.metadata'),
+            ]),
             (ds_boldreg_wf, outputnode, [('outputnode.xform', 'boldref2anat_xfm')]),
             (bold_reg_wf, summary, [('outputnode.fallback', 'fallback')]),
         ])  # fmt:skip

fmriprep/workflows/bold/outputs.py

@@ -546,7 +546,7 @@ def init_ds_registration_wf(
     workflow = pe.Workflow(name=name)
 
     inputnode = pe.Node(
-        niu.IdentityInterface(fields=['source_files', 'xform']),
+        niu.IdentityInterface(fields=['source_files', 'xform', 'metadata']),
         name='inputnode',
     )
     outputnode = pe.Node(niu.IdentityInterface(fields=['xform']), name='outputnode')
@@ -574,15 +574,16 @@ def init_ds_registration_wf(
         mem_gb=DEFAULT_MEMORY_MIN_GB,
     )
 
-    # fmt:off
     workflow.connect([
         (inputnode, sources, [('source_files', 'in1')]),
-        (inputnode, ds_xform, [('xform', 'in_file'),
-                               ('source_files', 'source_file')]),
+        (inputnode, ds_xform, [
+            ('xform', 'in_file'),
+            ('source_files', 'source_file'),
+            ('metadata', 'meta_dict'),
+        ]),
         (sources, ds_xform, [('out', 'Sources')]),
         (ds_xform, outputnode, [('out_file', 'xform')]),
-    ])
-    # fmt:on
+    ])  # fmt:skip
 
     return workflow
 

fmriprep/workflows/bold/registration.py

@@ -128,6 +128,8 @@ def init_bold_reg_wf(
         Affine transform from T1 space to BOLD space (ITK format)
     fallback
         Boolean indicating whether BBR was rejected (mri_coreg registration returned)
+    metadata
+        Output metadata from the registration workflow
 
     See Also
     --------
@@ -154,7 +156,7 @@ def init_bold_reg_wf(
     )
 
     outputnode = pe.Node(
-        niu.IdentityInterface(fields=['itk_bold_to_t1', 'itk_t1_to_bold', 'fallback']),
+        niu.IdentityInterface(fields=['itk_bold_to_t1', 'itk_t1_to_bold', 'fallback', 'metadata']),
         name='outputnode',
     )
 
@@ -188,6 +190,7 @@ def init_bold_reg_wf(
             ('outputnode.itk_bold_to_t1', 'itk_bold_to_t1'),
             ('outputnode.itk_t1_to_bold', 'itk_t1_to_bold'),
             ('outputnode.fallback', 'fallback'),
+            ('outputnode.metadata', 'metadata'),
         ]),
     ])  # fmt:skip
 
@@ -268,6 +271,8 @@ def init_bbreg_wf(
         Affine transform from T1 space to BOLD space (ITK format)
     fallback
         Boolean indicating whether BBR was rejected (mri_coreg registration returned)
+    metadata
+        Output metadata from the registration workflow
 
     """
     from nipype.interfaces.freesurfer import BBRegister
@@ -309,7 +314,7 @@ def init_bbreg_wf(
         name='inputnode',
     )
     outputnode = pe.Node(
-        niu.IdentityInterface(['itk_bold_to_t1', 'itk_t1_to_bold', 'fallback']),
+        niu.IdentityInterface(['itk_bold_to_t1', 'itk_t1_to_bold', 'fallback', 'metadata']),
         name='outputnode',
     )
 
@@ -357,6 +362,9 @@ def init_bbreg_wf(
     merge_ltas = pe.Node(niu.Merge(2), name='merge_ltas', run_without_submitting=True)
     concat_xfm = pe.Node(ConcatenateXFMs(inverse=True), name='concat_xfm')
 
+    metadata = pe.Node(niu.Merge(2), run_without_submitting=True, name='metadata')
+    select_meta = pe.Node(niu.Select(index=0), run_without_submitting=True, name='select_meta')
+
     workflow.connect([
         (inputnode, merge_ltas, [('fsnative2t1w_xfm', 'in2')]),
         # Wire up the co-registration alternatives
@@ -365,10 +373,18 @@ def init_bbreg_wf(
         (merge_ltas, concat_xfm, [('out', 'in_xfms')]),
         (concat_xfm, outputnode, [('out_xfm', 'itk_bold_to_t1')]),
         (concat_xfm, outputnode, [('out_inv', 'itk_t1_to_bold')]),
+        # Wire up the metadata alternatives
+        (metadata, select_meta, [('out', 'inlist')]),
+        (select_meta, outputnode, [('out', 'metadata')]),
     ])  # fmt:skip
 
     # Do not initialize with header, use mri_coreg
     if bold2anat_init != 'header':
+        metadata.inputs.in2 = {
+            'GeneratedBy': [
+                {'Name': 'mri_coreg', 'Version': mri_coreg.interface.version or '<unknown>'}
+            ]
+        }
         workflow.connect([
             (inputnode, mri_coreg, [('subjects_dir', 'subjects_dir'),
                                     ('subject_id', 'subject_id'),
@@ -400,6 +416,12 @@ def init_bbreg_wf(
         (bbregister, transforms, [('out_lta_file', 'in1')]),
     ])  # fmt:skip
 
+    metadata.inputs.in1 = {
+        'GeneratedBy': [
+            {'Name': 'bbregister', 'Version': bbregister.interface.version or '<unknown>'}
+        ]
+    }
+
     # Short-circuit workflow building, use boundary-based registration
     if use_bbr is True:
         outputnode.inputs.fallback = False
@@ -413,6 +435,7 @@ def init_bbreg_wf(
         (transforms, compare_transforms, [('out', 'lta_list')]),
         (compare_transforms, outputnode, [('out', 'fallback')]),
         (compare_transforms, select_transform, [('out', 'index')]),
+        (compare_transforms, select_meta, [('out', 'index')]),
     ])  # fmt:skip
 
     return workflow
@@ -493,6 +516,8 @@ def init_fsl_bbr_wf(
         Affine transform from T1 space to BOLD space (ITK format)
     fallback
         Boolean indicating whether BBR was rejected (rigid FLIRT registration returned)
+    metadata
+        Output metadata from the registration workflow
 
     """
     from nipype.interfaces.freesurfer import MRICoreg
@@ -532,7 +557,7 @@ def init_fsl_bbr_wf(
         name='inputnode',
     )
     outputnode = pe.Node(
-        niu.IdentityInterface(['itk_bold_to_t1', 'itk_t1_to_bold', 'fallback']),
+        niu.IdentityInterface(['itk_bold_to_t1', 'itk_t1_to_bold', 'fallback', 'metadata']),
         name='outputnode',
     )
 
@@ -549,6 +574,9 @@ def init_fsl_bbr_wf(
             'T2w intermediate for FSL is not implemented, registering with T1w instead.'
         )
 
+    metadata = pe.Node(niu.Merge(2), run_without_submitting=True, name='metadata')
+    select_meta = pe.Node(niu.Select(index=0), run_without_submitting=True, name='select_meta')
+
     # Mask T1w_preproc with T1w_mask to make T1w_brain
     mask_t1w_brain = pe.Node(ApplyMask(), name='mask_t1w_brain')
 
@@ -565,6 +593,12 @@ def init_fsl_bbr_wf(
         mem_gb=DEFAULT_MEMORY_MIN_GB,
     )
 
+    metadata.inputs.in2 = {
+        'GeneratedBy': [
+            {'Name': 'mri_coreg', 'Version': mri_coreg.interface.version or '<unknown>'}
+        ]
+    }
+
     workflow.connect([
         (inputnode, mask_t1w_brain, [
             ('t1w_preproc', 'in_file'),
@@ -578,6 +612,9 @@ def init_fsl_bbr_wf(
             ('out_xfm', 'itk_bold_to_t1'),
             ('out_inv', 'itk_t1_to_bold'),
         ]),
+        # Wire up the metadata alternatives
+        (metadata, select_meta, [('out', 'inlist')]),
+        (select_meta, outputnode, [('out', 'metadata')]),
     ])  # fmt:skip
 
     # Short-circuit workflow building, use rigid registration
@@ -604,6 +641,10 @@ def init_fsl_bbr_wf(
         LOGGER.warning('FSLDIR unset - using packaged BBR schedule')
         flt_bbr.inputs.schedule = data.load('flirtsch/bbr.sch')
 
+    metadata.inputs.in1 = {
+        'GeneratedBy': [{'Name': 'flirt', 'Version': flt_bbr.interface.version or '<unknown>'}]
+    }
+
     workflow.connect([
         (inputnode, wm_mask, [('t1w_dseg', 'in_seg')]),
         (inputnode, flt_bbr, [('in_file', 'in_file')]),
@@ -658,6 +699,8 @@ def init_fsl_bbr_wf(
         (transforms, select_transform, [('out', 'inlist')]),
         (compare_transforms, select_transform, [('out', 'index')]),
         (select_transform, xfm2itk, [('out', 'in_xfm')]),
+        # Select metadata
+        (compare_transforms, select_meta, [('out', 'index')]),
     ])  # fmt:skip
 
     return workflow