📋 HPC Batch Job Instructions for QSIrecon

✅ Log on to HPC OOD

Dataset

You'll use the same dataset you worked with for QSIprep. But, in this case, you'll need the qsiprep derivatives as a basis for the reconstruction!

✅ In the termina, navigate to your mri_practice directory: Note the path to this directory (Use pwd to display the path), as you'll need it for the runqsirecon_dev.sh script.

Script

You will modify a script for running QSIrecon on your existing CAM003 data. QSIrecon is included in the qsiprep container.

Caution!

QSIprep has to finish successfully before you can run QSIrecon! Look for the sub-CAM003.html in the derivatives/qsiprep directory and ensure it says "No errors to report!" at the bottom of the report.

✅ The runqsirecon_dev.sh script should already be in your home bin directory, but if not, you can use the terminal to copy it again:

✅ Open runqsirecon.sh in the OOD editor and modify the email address, account name and export MRIS statements as you have done before.

✅ Save your modified batch job.

✅ I suggest switching to elgato.

🟢 dMRI 6: Pr: qsirecon