Merge pull request #237 from GhazalehManj/old_containers

Update 05_extract_to_share.sh
TIGRLab · Sep 19, 2024 · bb9624a · bb9624a
2 parents 959a3ac + 9baa152
commit bb9624a
Showing 1 changed file with 6 additions and 1 deletion.
diff --git 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/