sending only orientation not all cfg

FCP-INDI · Oct 3, 2024 · 022f036 · 022f036
1 parent 9095825
commit 022f036
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Showing 2 changed files with 3 additions and 3 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", cfg="RPI"):
+def create_lesion_preproc(wf_name="lesion_preproc", orientation="RPI"):
     """Process lesions masks.
 
     Lesion mask file is deobliqued and reoriented in the same way as the T1 in
@@ -133,7 +133,7 @@ def create_lesion_preproc(wf_name="lesion_preproc", cfg="RPI"):
         mem_x=(0.0115, "in_file", "t"),
     )
 
-    lesion_reorient.inputs.orientation = cfg.pipeline_setup["desired_orientation"]
+    lesion_reorient.inputs.orientation = orientation
     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}")
+            lesion_preproc = create_lesion_preproc(wf_name=f"lesion_preproc{symm}", cfg.pipeline_setup["desired_orientation"])
             wf.connect(inputNode, "lesion_mask", lesion_preproc, "inputspec.lesion")
             wf.connect(
                 lesion_preproc,