Fixing freesurfer-abcd brain masking

Author: birajstha

CPAC/anat_preproc/anat_preproc.py

@@ -1128,37 +1128,12 @@ def freesurfer_abcd_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
         name=f"wmparc_to_nifti_{pipe_num}",
     )
 
-    # Register wmparc file if ingressing FreeSurfer data
-    if strat_pool.check_rpool("pipeline-fs_xfm"):
-        wmparc_to_native = pe.Node(
-            Function(
-                input_names=["source_file", "target_file", "xfm", "out_file"],
-                output_names=["transformed_file"],
-                function=normalize_wmparc,
-            ),
-            name=f"wmparc_to_native_{pipe_num}",
-        )
-
-        wmparc_to_native.inputs.out_file = "wmparc_warped.mgz"
-
-        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")
-
-        wf.connect(wmparc_to_native, "transformed_file", wmparc_to_nifti, "in_file")
-
-    else:
-        node, out = strat_pool.get_data("pipeline-fs_wmparc")
-        wf.connect(node, out, wmparc_to_nifti, "in_file")
+    node, out = strat_pool.get_data("pipeline-fs_wmparc")
+    wf.connect(node, out, wmparc_to_nifti, "in_file")
 
     wmparc_to_nifti.inputs.args = "-rt nearest"
 
-    node, out = strat_pool.get_data("desc-preproc_T1w")
+    node, out = strat_pool.get_data("desc-restore_T1w")
     wf.connect(node, out, wmparc_to_nifti, "reslice_like")
 
     binary_mask = pe.Node(
@@ -1194,7 +1169,7 @@ def freesurfer_abcd_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
 
     wf.connect(binary_filled_mask, "out_file", brain_mask_to_t1_restore, "in_file")
 
-    node, out = strat_pool.get_data("desc-preproc_T1w")
+    node, out = strat_pool.get_data("desc-restore_T1w")
     wf.connect(node, out, brain_mask_to_t1_restore, "ref_file")
 
     outputs = {"space-T1w_desc-brain_mask": (brain_mask_to_t1_restore, "out_file")}
@@ -2028,7 +2003,7 @@ def brain_mask_acpc_freesurfer(wf, cfg, strat_pool, pipe_num, opt=None):
     option_key=["anatomical_preproc", "brain_extraction", "using"],
     option_val="FreeSurfer-ABCD",
     inputs=[
-        "desc-preproc_T1w",
+        "desc-restore_T1w",
         "pipeline-fs_wmparc",
         "pipeline-fs_raw-average",
         "pipeline-fs_xfm",

CPAC/anat_preproc/utils.py

@@ -487,7 +487,7 @@ def mri_convert(in_file, reslice_like=None, out_file=None, args=None):
     import os
 
     if out_file is None:
-        out_file = in_file.replace(".mgz", ".nii.gz")
+        out_file = os.path.join(os.getcwd(), os.path.basename(in_file).replace(".mgz", ".nii.gz"))
 
     cmd = "mri_convert %s %s" % (in_file, out_file)
 
@@ -525,7 +525,7 @@ def mri_convert_reorient(in_file, orientation, out_file=None):
     import os
 
     if out_file is None:
-        out_file = in_file.split(".")[0] + "_reoriented.mgz"
+        out_file = os.path.join(os.getcwd(), os.path.basename(in_file).split(".")[0] + "_reoriented.mgz")
 
     cmd = "mri_convert %s %s --out_orientation %s" % (in_file, out_file, orientation)