From 9baa152699318623d351a5db171846c7d71e8c0f Mon Sep 17 00:00:00 2001
From: GhazalehManj <126309136+GhazalehManj@users.noreply.github.com>
Date: Wed, 18 Sep 2024 21:52:02 -0400
Subject: [PATCH] Update 05_extract_to_share.sh

---
 code/05_extract_to_share.sh | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/code/05_extract_to_share.sh b/code/05_extract_to_share.sh
index bfc0ded..34110e7 100644
--- a/code/05_extract_to_share.sh
+++ b/code/05_extract_to_share.sh
@@ -73,11 +73,16 @@ echo "copying over the ciftify qc images"
 
 mkdir ${PROJECT_DIR}/data/share/ciftify
 
+singularity exec --cleanenv \
+  -B ${PROJECT_DIR}/data/local/bids:/bids \
+  -B ${PROJECT_DIR}/data/local/ciftify:/derived \
+  ${PROJECT_DIR}/containers/fmriprep_ciftity-v1.3.2-2.3.3.simg \
+  cifti_vis_recon_all index --ciftify-work-dir /derived
+
 ## copy over the ciftify QC outputs
 rsync -a ${PROJECT_DIR}/data/local/ciftify/qc_recon_all  ${PROJECT_DIR}/data/share/ciftify/
 
 
-
 ## copy over the Enigma_extract outputs
 echo "copying over the ENIGMA extracted cortical and subcortical files"
 rsync -a ${PROJECT_DIR}/data/local/ENIGMA_extract ${PROJECT_DIR}/data/share/