From eee28c1f1a83bd573c89ba8ae214be527fd2949f Mon Sep 17 00:00:00 2001
From: Alexandru Foias <afoias@polymtl.ca>
Date: Mon, 20 Dec 2021 12:00:19 -0500
Subject: [PATCH 1/2] remove sub-config.yml

---
 sub-config.yml | 8 --------
 1 file changed, 8 deletions(-)
 delete mode 100644 sub-config.yml

diff --git a/sub-config.yml b/sub-config.yml
deleted file mode 100644
index eb0f60e..0000000
--- a/sub-config.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-subjects:
-    sub-001DAH:
-        T1w: run-02
-        FLAIR: run-01
-    sub-002OEI:
-        FLAIR: run-01
-    sub-003THV:
-        FLAIR: run-01
\ No newline at end of file

From a876d8a8b2822be61d834429bf9d5d123560f7de Mon Sep 17 00:00:00 2001
From: Alexandru Foias <afoias@polymtl.ca>
Date: Mon, 20 Dec 2021 12:43:34 -0500
Subject: [PATCH 2/2] fix name of config file in process_data

---
 process_data.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/process_data.sh b/process_data.sh
index b843ce9..d89d349 100755
--- a/process_data.sh
+++ b/process_data.sh
@@ -109,7 +109,7 @@ segment_gm_if_does_not_exist(){
 select_subject_data(){
   arg1=$1
   arg2=$2
-  CONTRAST_CONFIG="$(cat $PATH_DATA/sub-config.yml | shyaml get-value subjects.$1.$2 '')"
+  CONTRAST_CONFIG="$(cat $PATH_DATA/include.yml | shyaml get-value subjects.$1.$2 '')"
   # echo Please enter the path of the subjects yaml
   # read path_subjects_yaml
 }