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1. Approach 1 Instruction

Step 1. Build an Artemis-compatible Singularity container.

Containers on Artemis need to have /project and /scratch directories, otherwise we cannot bind mount Artemis's /project and /scratch filesystems inside of your container. If you are running GPU jobs, you should also make sure the file /usr/bin/nvidia-smi exists. It doesn't have to be the actual nvidia-smi binary, but can be a blank file.

Step 2. Logon to Artemis and pull data from XNAT, please refer to below link

XNAT REST API Manuals, Artemis (HPC) and examples

Step 3. Edit your PBS script to run the Singularity Image

Sample PBS Script

#!/bin/bash
#PBS -P PROJECTNAME
#PBS -l select=1:ncpus=1:mem=1gb
#PBS -l walltime=1:00:00
#PBS -M EmailAddress
#PBS -m abe
#PBS -j oe

module load singularity
mkdir -p /scratch/PROJECTNAME/NIFTI
singularity exec dcm2niix.simg dcm2niix -o /scratch/PROJECTNAME/NIFTI/ /scratch/PROJECTNAME/DICOM/files

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https://singularity.lbl.gov/user-guide

Step 4. When the job has completed, please refer the below document to push the data back to XNAT from Artemis 

XNAT REST API Manuals, Artemis (HPC) and examples

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