From 4bc891b1304078ef64ea6efb55115847de832ebe Mon Sep 17 00:00:00 2001
From: Ali Khan <alik@robarts.ca>
Date: Wed, 8 Jan 2025 12:20:47 -0500
Subject: [PATCH] fix for myelin maps sampled on nativesurf

also adds a dryrun test (since this was in github actions tests already)
---
 .dryrun_test_all.sh                      |  1 +
 hippunfold/workflow/rules/myelin_map.smk | 12 ++++--------
 2 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/.dryrun_test_all.sh b/.dryrun_test_all.sh
index f6deb448..2eca2d73 100755
--- 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
index 573580fd..3c9eab70 100644
--- a/hippunfold/workflow/rules/myelin_map.smk
+++ b/hippunfold/workflow/rules/myelin_map.smk
@@ -83,9 +83,8 @@ 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}",
@@ -93,9 +92,8 @@ rule sample_myelin_map_surf:
             **inputs.subj_wildcards
         ),
         inner=bids(
-            root=root,
+            root=work,
             datatype="surf",
-            den="{density}",
             suffix="inner.surf.gii",
             space="corobl",
             hemi="{hemi}",
@@ -103,9 +101,8 @@ rule sample_myelin_map_surf:
             **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