grouped outlier opts

Author: Jordan DeKraker

hippunfold/config/snakebids.yml

@@ -366,12 +366,13 @@ cifti_metric_types:
     - curvature.dscalar
 
 # params for detecting and removing outlier vertices
-outlierSmoothDist: 
-  unfoldiso: 15
-  0p5mm: 7
-  1mm: 3
-  2mm: 1
-vertexOutlierThreshold: 3
+outlier_opts:
+  outlierSmoothDist: 
+    unfoldiso: 15
+    0p5mm: 7
+    1mm: 3
+    2mm: 1
+  vertexOutlierThreshold: 3
 
 
 
@@ -627,7 +628,7 @@ unfold_vol_ref:
 unfold_crop_epsilon_fractions:
     - 0
     - 0
-    - 1
+    - 1 #in unfolded space voxels
 
 # space for uniform unfolded grid:
 #  currently only used for interpolating hipp subfields on surface

hippunfold/workflow/rules/gifti.smk

@@ -214,8 +214,8 @@ rule correct_bad_vertices1:
             **config["subj_wildcards"]
         ),
     params:
-        dist=lambda wildcards: config["outlierSmoothDist"][wildcards.density],
-        threshold=config["vertexOutlierThreshold"],
+        dist=lambda wildcards: config["outlier_opts"]["outlierSmoothDist"][wildcards.density],
+        threshold=config["outlier_opts"]["vertexOutlierThreshold"],
     output:
         gii=bids(
             root=work,
@@ -764,8 +764,8 @@ rule correct_bad_vertices2:
             **config["subj_wildcards"]
         ),
     params:
-        dist=lambda wildcards: config["outlierSmoothDist"][wildcards.density],
-        threshold=config["vertexOutlierThreshold"],
+        dist=lambda wildcards: config["outlier_opts"]["outlierSmoothDist"][wildcards.density],
+        threshold=config["outlier_opts"]["vertexOutlierThreshold"],
     output:
         gii=bids(
             root=work,