xnat-tools-examples

Sample scripts invoking xnat-tools.

Getting started in Oscar

Please clone this repository. If this is your first time working with xnat-tools, you can use BNC's shared folder in Oscar.

Set-up the scripts

1. Login into Oscar

2. In the terminal navigate into the directory where you will download this code

   cd /gpfs/data/bnc/shared/xnat-tools-examples
   

3. Clone this repository

   git clone https://github.com/brown-bnc/xnat-tools-examples.git $USER
   

4. Make a logs directory

   cd $USER
   mkdir -m 775 logs
   

5. Navigate to scripts folder

   cd oscar-sbatch
   

6. Set-up variables/secrets

   Create a .env file inside the current directory and place your secrets

   ⚠️ At the end of this session you should delete the file, or at least your password

   XNAT_USER=<user>
   XNAT_PASSWORD=<psswd>
   XNAT_SESSION=<xnat_session_accession_number>
   

   ⚠️ If you your code and data does not live in /gpfs/data/bnc/shared then you also need to make sure that data_dir, bids_root_dir and bidsmap_file inside xnat2bids_single_session.sh are correct

7. Run script

   sbatch xnat2bids_single_session.sh
   

8. View logs

   cat ../logs/<jobid>.txt