fixed positions of args in lesion_preproc and added default RPI

FCP-INDI · Oct 3, 2024 · 96f5871 · 96f5871
1 parent 022f036
commit 96f5871
Show file tree

Hide file tree

Showing 3 changed files with 6 additions and 4 deletions.
diff --git a/CPAC/anat_preproc/lesion_preproc.py b/CPAC/anat_preproc/lesion_preproc.py
@@ -58,7 +58,7 @@ def inverse_lesion(lesion_path):
     return lesion_out
 
 
-def create_lesion_preproc(wf_name="lesion_preproc", orientation="RPI"):
+def create_lesion_preproc(cfg=None, wf_name="lesion_preproc"):
     """Process lesions masks.
 
     Lesion mask file is deobliqued and reoriented in the same way as the T1 in
@@ -133,7 +133,9 @@ def create_lesion_preproc(wf_name="lesion_preproc", orientation="RPI"):
         mem_x=(0.0115, "in_file", "t"),
     )
 
-    lesion_reorient.inputs.orientation = orientation
+    lesion_reorient.inputs.orientation = (
+        cfg.pipeline_setup["desired_orientation"] if cfg else "RPI"
+    )
     lesion_reorient.inputs.outputtype = "NIFTI_GZ"
 
     preproc.connect(lesion_deoblique, "out_file", lesion_reorient, "in_file")

diff --git a/CPAC/registration/registration.py b/CPAC/registration/registration.py
@@ -1736,7 +1736,7 @@ def ANTs_registration_connector(
             "ANTs"
         ]["use_lesion_mask"]:
             # Create lesion preproc node to apply afni Refit and Resample
-            lesion_preproc = create_lesion_preproc(wf_name=f"lesion_preproc{symm}", cfg.pipeline_setup["desired_orientation"])
+            lesion_preproc = create_lesion_preproc(cfg, wf_name=f"lesion_preproc{symm}")
             wf.connect(inputNode, "lesion_mask", lesion_preproc, "inputspec.lesion")
             wf.connect(
                 lesion_preproc,

diff --git a/CPAC/registration/tests/test_registration.py b/CPAC/registration/tests/test_registration.py
@@ -130,7 +130,7 @@ def test_registration_lesion():
 
     anat_preproc.inputs.inputspec.anat = anat_file
 
-    lesion_preproc = create_lesion_preproc(wf_name="lesion_preproc")
+    lesion_preproc = create_lesion_preproc(cfg, wf_name="lesion_preproc")
 
     lesion_preproc.inputs.inputspec.lesion = lesion_file