make native surf the default

khanlab · Dec 30, 2024 · f56a43b · f56a43b
1 parent 5ae5a8d
commit f56a43b
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Showing 2 changed files with 1 addition and 10 deletions.
diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml
@@ -194,12 +194,6 @@ parse_args:
     default: False
     action: store_true
 
-  --native_surf:
-    help: 'Use native surf workflow to generate isosurfaces in native space, and use wb_command tools to resample. Note: this currently disables unfolded registration if applied (until it is implemented).'
-    default: False
-    action: store_true
-
-
   --generate_myelin_map:
     help: 'Generate myelin map using T1w divided by T2w, and map to surface with ribbon approach. Requires both T1w and T2w images to be present. (default: %(default)s)'
     default: False
@@ -703,4 +697,3 @@ generate_myelin_map: False
 root: results
 use_template_seg: False
 template_seg_smoothing_factor: 2
-native_surf: False
diff --git a/hippunfold/workflow/Snakefile b/hippunfold/workflow/Snakefile
@@ -144,9 +144,7 @@ include: "rules/qc.smk"
 include: "rules/myelin_map.smk"
 
 
-if config["native_surf"]:
-
-    include: "rules/native_surf.smk"
+include: "rules/native_surf.smk"
 
 
 if config["use_template_seg"]: