From ef873ea0c6712fbbabc628063fbb91972bc94c4e Mon Sep 17 00:00:00 2001
From: Parker Singleton <sps253@cornell.edu>
Date: Mon, 16 Dec 2024 15:20:12 -0500
Subject: [PATCH] update paths

---
 curation/dcm2bids/dcm2bids_submit.sh | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/curation/dcm2bids/dcm2bids_submit.sh b/curation/dcm2bids/dcm2bids_submit.sh
index 779c1b7..dc4662b 100644
--- a/curation/dcm2bids/dcm2bids_submit.sh
+++ b/curation/dcm2bids/dcm2bids_submit.sh
@@ -4,21 +4,20 @@
 #SBATCH --time=24:00:00                 # Maximum runtime
 #SBATCH --cpus-per-task=4               # Number of CPUs per task
 #SBATCH --mem=8G                        # Memory per job
-#SBATCH --output=/cbica/projects/grmpy/data/bids/code/dcm2bids/logs/dcm2bids_%A_%a.out # Output log
-#SBATCH --error=/cbica/projects/grmpy/data/bids/code/dcm2bids/logs/dcm2bids_%A_%a.err  # Error log
+#SBATCH --output=/cbica/projects/grmpy/code/curation/dcm2bids/logs/dcm2bids_%A_%a.out # Output log
+#SBATCH --error=/cbica/projects/grmpy/code/curation/dcm2bids/logs/dcm2bids_%A_%a.err  # Error log
 
 # Define paths
 bids="/cbica/projects/grmpy/data/bids"
 
 # Step 1: Get all subject IDs
-# subjects=($(ls -d ${bids}/sourcedata/GRMPY_822831/SUBJECTS/* | xargs -n 1 basename))
-subjects=("95257" "20120")  # For debugging
+subjects=($(ls -d /cbica/projects/grmpy/sourcedata/GRMPY_822831/SUBJECTS/* | xargs -n 1 basename))
 
 # Step 2: Select the current subject based on the SLURM array task ID
 subID=${subjects[${SLURM_ARRAY_TASK_ID}]}
 
 # Step 3: Find all DICOM directories for all sessions of the current subject
-mapfile -t session_dirs < <(find ${bids}/sourcedata/GRMPY_822831/SUBJECTS/${subID}/SESSIONS/*/ACQUISITIONS -maxdepth 0 -type d)
+mapfile -t session_dirs < <(find /cbica/projects/grmpy/sourcedata/GRMPY_822831/SUBJECTS/${subID}/SESSIONS/*/ACQUISITIONS -maxdepth 0 -type d)
 
 # Step 4: Process each session
 session_num=1  # Initialize session counter
@@ -28,7 +27,7 @@ for session_dir in "${session_dirs[@]}"; do
 
     ~/miniforge3/envs/dcmconv/bin/dcm2bids -p ${subID} \
         -s ${session_num} \
-        -c ${bids}/code/dcm2bids/config.json \
+        -c /cbica/projects/grmpy/code/dcm2bids/config.json \
         -o ${bids} \
         -d ${session_dir} \
         --force_dcm2bids