adding match fov to bring fs brain mask to T1w space

Author: birajstha

CPAC/anat_preproc/anat_preproc.py

@@ -1322,17 +1322,30 @@ def freesurfer_fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
 
     wf.connect(combine_mask, "out_file", binarize_combined_mask, "in_file")
 
+    # CCS brain mask is in FS space, transfer it back to native T1 space 
+    match_fov_ccs_brain_mask = pe.Node(
+        interface=fsl.FLIRT(), name=f"match_fov_CCS_brain_mask_{node_id}"
+    )
+    match_fov_ccs_brain_mask.inputs.apply_xfm = True
+    match_fov_ccs_brain_mask.inputs.uses_qform = True
+    match_fov_ccs_brain_mask.inputs.interp = "nearestneighbour"
+
+    node, out = strat_pool.get_data("pipeline-fs_raw-average")
+    wf.connect(node, out, match_fov_ccs_brain_mask, "reference")
+
+    wf.connect(binarize_combined_mask, "out_file", match_fov_ccs_brain_mask, "in_file")
+
     if opt == "FreeSurfer-BET-Tight":
         outputs = {
             "space-T1w_desc-tight_brain_mask": (
-                binarize_combined_mask,
+                match_fov_ccs_brain_mask,
                 "out_file",
             )
         }
     elif opt == "FreeSurfer-BET-Loose":
         outputs = {
             "space-T1w_desc-loose_brain_mask": (
-                binarize_combined_mask,
+                match_fov_ccs_brain_mask,
                 "out_file",
             )
         }