fix for myelin maps sampled on nativesurf

also adds a dryrun test (since this was in github actions tests already)
khanlab · Jan 8, 2025 · 4bc891b · 4bc891b
1 parent f76bba6
commit 4bc891b
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Showing 2 changed files with 5 additions and 8 deletions.
diff --git a/.dryrun_test_all.sh b/.dryrun_test_all.sh
@@ -14,3 +14,4 @@ hippunfold test_data/bids_manualseg_1hemi test_out participant -np --modality ma
 hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template 
 hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w 
 hippunfold test_data/bids_T1w test_out participant -np --modality T1w --use-template-seg 
+hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --generate-myelin-map
diff --git a/hippunfold/workflow/rules/myelin_map.smk b/hippunfold/workflow/rules/myelin_map.smk
@@ -83,29 +83,26 @@ rule sample_myelin_map_surf:
             **inputs.subj_wildcards
         ),
         mid=bids(
-            root=root,
+            root=work,
             datatype="surf",
-            den="{density}",
             suffix="midthickness.surf.gii",
             space="corobl",
             hemi="{hemi}",
             label="{autotop}",
             **inputs.subj_wildcards
         ),
         inner=bids(
-            root=root,
+            root=work,
             datatype="surf",
-            den="{density}",
             suffix="inner.surf.gii",
             space="corobl",
             hemi="{hemi}",
             label="{autotop}",
             **inputs.subj_wildcards
         ),
         outer=bids(
-            root=root,
+            root=work,
             datatype="surf",
-            den="{density}",
             suffix="outer.surf.gii",
             space="corobl",
             hemi="{hemi}",
@@ -126,9 +123,8 @@ rule sample_myelin_map_surf:
         metric=bids(
             root=root,
             datatype="surf",
-            den="{density}",
             suffix="myelin.shape.gii",
-            space="{space}",
+            space="corobl",
             hemi="{hemi}",
             label="{autotop}",
             **inputs.subj_wildcards