Merge pull request #1924 from e-kenneally/fix/fs_ingress

🐛 Fix FreeSurfer ingress misalignment

Author: sgiavasis

CPAC/anat_preproc/anat_preproc.py

@@ -914,6 +914,24 @@ def freesurfer_abcd_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
     ### ABCD harmonization - anatomical brain mask generation ###
     # Ref: https://github.com/DCAN-Labs/DCAN-HCP/blob/master/PostFreeSurfer/PostFreeSurferPipeline.sh#L151-L156
 
+    wmparc_to_native = pe.Node(
+        interface=freesurfer.ApplyVolTransform(),
+        name='wmparc_to_native')
+    
+    wmparc_to_native.inputs.reg_header = True
+
+    node, out = strat_pool.get_data('pipeline-fs_wmparc') 
+    wf.connect(node, out, wmparc_to_native, 'source_file')
+
+    node, out = strat_pool.get_data('pipeline-fs_raw-average')
+    wf.connect(node, out, wmparc_to_native, 'target_file')
+
+    node, out = strat_pool.get_data('pipeline-fs_xfm')
+    wf.connect(node, out, wmparc_to_native, 'xfm_reg_file')
+
+    node, out = strat_pool.get_data('freesurfer-subject-dir')
+
+    wf.connect(node, out, wmparc_to_native, 'subjects_dir')
     wmparc_to_nifti = pe.Node(util.Function(input_names=['in_file',
                                                          'reslice_like',
                                                          'args'],
@@ -922,8 +940,7 @@ def freesurfer_abcd_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
                               name=f'wmparc_to_nifti_{pipe_num}')
     wmparc_to_nifti.inputs.args = '-rt nearest'
 
-    node, out = strat_pool.get_data('pipeline-fs_wmparc')
-    wf.connect(node, out, wmparc_to_nifti, 'in_file')
+    wf.connect(wmparc_to_native, 'transformed_file', wmparc_to_nifti, 'in_file')
 
     node, out = strat_pool.get_data('desc-preproc_T1w')
     wf.connect(node, out, wmparc_to_nifti, 'reslice_like')
@@ -1772,6 +1789,8 @@ def brain_mask_freesurfer_abcd(wf, cfg, strat_pool, pipe_num, opt=None):
      "option_val": "FreeSurfer-ABCD",
      "inputs": ["desc-preproc_T1w",
                 "pipeline-fs_wmparc",
+                "pipeline-fs_raw-average",
+                "pipeline-fs_xfm",
                 "freesurfer-subject-dir"],
      "outputs": ["space-T1w_desc-brain_mask"]}
     '''
@@ -1813,6 +1832,8 @@ def brain_mask_acpc_freesurfer_abcd(wf, cfg, strat_pool, pipe_num, opt=None):
      "option_val": "FreeSurfer-ABCD",
      "inputs": ["desc-preproc_T1w",
                 "pipeline-fs_wmparc",
+                "pipeline-fs_raw-average",
+                "pipeline-fs_xfm",
                 "freesurfer-subject-dir"],
      "outputs": ["space-T1w_desc-acpcbrain_mask"]}
     '''
@@ -2565,7 +2586,6 @@ def freesurfer_abcd_preproc(wf, cfg, strat_pool, pipe_num, opt=None):
                  "pipeline-fs_wmparc",
                  "freesurfer-subject-dir"]}
     '''
-
     # fnirt-based brain extraction
     brain_extraction = fnirt_based_brain_extraction(config=cfg,
                                                     wf_name=f'fnirt_based_brain_extraction_{pipe_num}')
@@ -2666,6 +2686,7 @@ def freesurfer_abcd_preproc(wf, cfg, strat_pool, pipe_num, opt=None):
         return (wf, outputs)
 
     else:
+        
         ### recon-all -all step ###
         reconall = pe.Node(interface=freesurfer.ReconAll(),
                            name=f'anat_freesurfer_{pipe_num}',

CPAC/pipeline/engine.py

@@ -1721,6 +1721,7 @@ def ingress_raw_anat_data(wf, rpool, cfg, data_paths, unique_id, part_id,
             'pipeline-fs_hemi-R_desc-surfaceMap_volume': 'surf/rh.volume',
             'pipeline-fs_hemi-L_desc-surfaceMesh_white': 'surf/lh.white',
             'pipeline-fs_hemi-R_desc-surfaceMesh_white': 'surf/rh.white',
+            'pipeline-fs_xfm': 'mri/transforms/talairach.xfm'
         }
 
         for key, outfile in recon_outs.items():

CPAC/seg_preproc/seg_preproc.py

@@ -796,7 +796,9 @@ def tissue_seg_freesurfer(wf, cfg, strat_pool, pipe_num, opt=None):
      "switch": ["run"],
      "option_key": ["tissue_segmentation", "using"],
      "option_val": "FreeSurfer",
-     "inputs": ["freesurfer-subject-dir"],
+     "inputs": ["freesurfer-subject-dir", 
+                 "pipeline-fs_raw-average",
+                 "pipeline-fs_subcortical-seg"],
      "outputs": ["pipeline-fs_hemi-L_desc-surface_curv",
                  "pipeline-fs_hemi-R_desc-surface_curv", 
                  "pipeline-fs_hemi-L_desc-surfaceMesh_pial",
@@ -818,12 +820,30 @@ def tissue_seg_freesurfer(wf, cfg, strat_pool, pipe_num, opt=None):
                  "label-WM_mask"]}
     '''
 
+    node, out = strat_pool.get_data('freesurfer-subject-dir')
+
+    fs_aseg_to_native = pe.Node(interface=freesurfer.ApplyVolTransform(),
+                                name=f'fs_aseg_to_native_{pipe_num}')
+    fs_aseg_to_native.inputs.reg_header = True
+    fs_aseg_to_native.inputs.interp = 'nearest'
+
+    wf.connect(node, out, fs_aseg_to_native, 'subjects_dir')
+
+    node, out = strat_pool.get_data('pipeline-fs_subcortical-seg')
+    wf.connect(node, out, fs_aseg_to_native, 'source_file')
+
+    node, out = strat_pool.get_data('pipeline-fs_raw-average')
+    wf.connect(node, out, fs_aseg_to_native, 'target_file')
+
     fs_aseg_to_nifti = pe.Node(util.Function(input_names=['in_file'],
                                              output_names=['out_file'],
                                              function=mri_convert),
                                name=f'fs_aseg_to_nifti_{pipe_num}')
     fs_aseg_to_nifti.inputs.args = '-rt nearest'
 
+    wf.connect(fs_aseg_to_native, 'transformed_file',
+               fs_aseg_to_nifti, 'in_file')
+
     pick_tissue = pe.Node(pick_tissue_from_labels_file_interface(),
                           name=f'select_fs_tissue_{pipe_num}')