Fixing freesurfer-abcd brain masking

CHANGELOG.md

@@ -72,6 +72,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Lingering calls to `cpac_outputs.csv` (was changed to `cpac_outputs.tsv` in v1.8.1).
 - A bug in the `freesurfer_abcd_preproc` nodeblock where the `Template` image was incorrectly used as `reference` during the `inverse_warp` step. Replacing it with the subject-specific `T1w` image resolved the issue of the `desc-restoreBrain_T1w` being chipped off.
 - A bug in `ideal_bandpass` where the frequency mask was incorrectly applied, which caused filter to fail in certain cases.
+- `Freesufer-ABCD` brain masking strategy to create mask as per the original DCAN script.
 - A bug where `$ANTSPATH` was unset in C-PAC with FreeSurfer images.
 
 ### Upgraded dependencies

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", "desc-preproc_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", "desc-preproc_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")}
@@ -2010,10 +1985,9 @@ 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", "desc-preproc_T1w"],
         "pipeline-fs_wmparc",
         "pipeline-fs_raw-average",
-        "pipeline-fs_xfm",
         "freesurfer-subject-dir",
     ],
     outputs=["space-T1w_desc-brain_mask"],
@@ -2067,10 +2041,9 @@ def brain_mask_freesurfer_fsl_tight(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", "desc-preproc_T1w"],
         "pipeline-fs_wmparc",
         "pipeline-fs_raw-average",
-        "pipeline-fs_xfm",
         "freesurfer-subject-dir",
     ],
     outputs=["space-T1w_desc-acpcbrain_mask"],

CPAC/anat_preproc/utils.py

@@ -487,7 +487,9 @@ 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 +527,9 @@ 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)
 

CPAC/pipeline/engine.py

@@ -2062,7 +2062,6 @@ def ingress_freesurfer(wf, rpool, cfg, data_paths, unique_id, part_id, ses_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.lta",
     }
 
     for key, outfile in recon_outs.items():