replaced RPI to take in config value in few more places

FCP-INDI · Oct 2, 2024 · c593895 · c593895
1 parent 70ec24b
commit c593895
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/CPAC/anat_preproc/lesion_preproc.py b/CPAC/anat_preproc/lesion_preproc.py
@@ -19,6 +19,7 @@
 import nipype.interfaces.utility as util
 
 from CPAC.pipeline import nipype_pipeline_engine as pe
+from CPAC.utils.configuration import Configuration as cfg
 from CPAC.utils.interfaces import Function
 
 
@@ -133,7 +134,7 @@ def create_lesion_preproc(wf_name="lesion_preproc"):
         mem_x=(0.0115, "in_file", "t"),
     )
 
-    lesion_reorient.inputs.orientation = "RPI"
+    lesion_reorient.inputs.orientation = cfg.pipeline_setup["desired_orientation"]
     lesion_reorient.inputs.outputtype = "NIFTI_GZ"
 
     preproc.connect(lesion_deoblique, "out_file", lesion_reorient, "in_file")

diff --git a/CPAC/func_preproc/func_preproc.py b/CPAC/func_preproc/func_preproc.py
@@ -1290,7 +1290,7 @@ def bold_mask_anatomical_refined(wf, cfg, strat_pool, pipe_num, opt=None):
         mem_x=(0.0115, "in_file", "t"),
     )
 
-    func_reorient.inputs.orientation = "RPI"
+    func_reorient.inputs.orientation = cfg.pipeline_setup["desired_orientation"]
     func_reorient.inputs.outputtype = "NIFTI_GZ"
 
     wf.connect(func_deoblique, "out_file", func_reorient, "in_file")