From 30a0076531f33e1be96572dc318dc7b7da45d33e Mon Sep 17 00:00:00 2001
From: singlesp <sps253@cornell.edu>
Date: Mon, 16 Dec 2024 15:13:21 -0500
Subject: [PATCH] first commit

---
 .gitignore                            |  5 ++++
 curation/dcm2bids/dcm2bids_submit.sh  | 35 ++++++++++++++++++++++++
 curation/dcm2bids/dcm2bids_submit2.sh | 38 +++++++++++++++++++++++++++
 3 files changed, 78 insertions(+)
 create mode 100644 curation/dcm2bids/dcm2bids_submit.sh
 create mode 100644 curation/dcm2bids/dcm2bids_submit2.sh

diff --git a/.gitignore b/.gitignore
index 55044b9..8d3f918 100644
--- a/.gitignore
+++ b/.gitignore
@@ -203,3 +203,8 @@ vignettes/*.pdf
 
 # R Environment Variables
 .Renviron
+
+# log files
+log/
+/log/
+**/log/
diff --git a/curation/dcm2bids/dcm2bids_submit.sh b/curation/dcm2bids/dcm2bids_submit.sh
new file mode 100644
index 0000000..b62ef1c
--- /dev/null
+++ b/curation/dcm2bids/dcm2bids_submit.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+#SBATCH --job-name=dcm2bids_conversion  # Job name
+#SBATCH --array=0-230
+#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
+
+# Define paths
+bids="/cbica/projects/grmpy/data/bids"
+
+# Step 1: Get all subject IDs
+subjects=($(ls -d ${bids}/sourcedata/GRMPY_822831/SUBJECTS/* | xargs -n 1 basename))
+
+# Step 2: Select the current subject based on the SLURM array task ID
+subID=${subjects[${SLURM_ARRAY_TASK_ID}]}
+
+# Step 3: Find all DICOM directories for all sessions of the current subject
+session_dirs=$(find ${bids}/sourcedata/GRMPY_822831/SUBJECTS/${subID}/SESSIONS/*/ACQUISITIONS -maxdepth 0 -type d)
+
+# Step 4: Process each session
+session_num=1  # Initialize session counter
+for session_dir in "${session_dirs[@]}"; do
+
+    ~/miniforge3/envs/dcmconv/bin/dcm2bids -p ${subID} \
+        -s ${session_num} \
+        -c ${bids}/code/dcm2bids/config.json \
+        -o ${bids} \
+        -d ${session_dir} \
+        --force_dcm2bids
+        
+    ((session_num++))
+    
+done
diff --git a/curation/dcm2bids/dcm2bids_submit2.sh b/curation/dcm2bids/dcm2bids_submit2.sh
new file mode 100644
index 0000000..779c1b7
--- /dev/null
+++ b/curation/dcm2bids/dcm2bids_submit2.sh
@@ -0,0 +1,38 @@
+#!/bin/bash
+#SBATCH --job-name=dcm2bids_conversion  # Job name
+#SBATCH --array=0-1
+#SBATCH --time=24:00:00                 # Maximum runtime
+#SBATCH --cpus-per-task=4               # Number of CPUs per task
+#SBATCH --mem=8G                        # Memory per job
+#SBATCH --output=/cbica/projects/grmpy/data/bids/code/dcm2bids/logs/dcm2bids_%A_%a.out # Output log
+#SBATCH --error=/cbica/projects/grmpy/data/bids/code/dcm2bids/logs/dcm2bids_%A_%a.err  # Error log
+
+# Define paths
+bids="/cbica/projects/grmpy/data/bids"
+
+# Step 1: Get all subject IDs
+# subjects=($(ls -d ${bids}/sourcedata/GRMPY_822831/SUBJECTS/* | xargs -n 1 basename))
+subjects=("95257" "20120")  # For debugging
+
+# Step 2: Select the current subject based on the SLURM array task ID
+subID=${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)
+
+# Step 4: Process each session
+session_num=1  # Initialize session counter
+for session_dir in "${session_dirs[@]}"; do
+
+    echo "Processing session ${session_num} for subject ${subID} in directory ${session_dir}"  # For debugging
+
+    ~/miniforge3/envs/dcmconv/bin/dcm2bids -p ${subID} \
+        -s ${session_num} \
+        -c ${bids}/code/dcm2bids/config.json \
+        -o ${bids} \
+        -d ${session_dir} \
+        --force_dcm2bids
+        
+    ((session_num++))
+    
+done