Using mriqc with neurodesk on HPC

Using mriqc with neurodesk on HPC#

A brief guide to using mriqc with neurodesk.

This tutorial was created by Kelly G. Garner.

Github: @kel_github

This workflow documents how to use MRIQC with neurodesk and provides some details that may help you troubleshoot some common problems I found along the way.

Getting Set Up with Neurodesk

Assumptions#

  • [ ] Your data is already in BIDS format

  • [ ] You plan to run mriqc using Neurodesk

NOTE: MRIQC has its $HOME variable hardcoded to be /home/mriqc. This leads to problems on some HPCs. A workaround is to run this before mriqc:

export neurodesk_singularity_opts="--home $HOME:/home"

Steps#

Launch Neurodesk#

From the launcher, click the Neurodesktop icon:

launch_neurodesk

Open MRIQC#

Now you’re in Neurodesk, use the menus to first open the neurodesk options

neurodesk_menu

and then select MRIQC. Note that the latest version will be the lowest on the dropdown list:

open_mriqc

This will open a terminal window where MRIQC is ready and waiting at your fingertips - woohoo!

mriqc_bash

Setting up mriqc command#

You can now enter the following mriqc commands straight into the command line in the newly opened terminal window.

export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=6 # specify the number of threads you want to use

mriqc /path/to/your/data \ # this is the top level of your data folder
         /path/to/your/data/derivatives \ # where you want mriqc output to be saved
         participant \ # this tells mriqc to analyse at the participant level
         --participant-label 01 \ # put what ever participant labels you want to analyse
         --work-dir /path/to/work/directory \ #useful to specify so your home directory definitely does not get clogged
         --nprocs 6 --mem_gb 10000 \ # mriqc can be greedy on the hpc, make sure it is not
         -v # be verbal mriqc, tell me what you are doing

Note that above I have set the processor and memory limits. This is because I was in this case running on an HPC, and I used those commands to stop MRIQC from hogging all the resources. You may want to skip those inputs if you’re running MRIQC locally.

OR: if you have run all the participants and you just want the group level report, use these mriqc commands instead:

mriqc /path/to/your/data \ # this is the top level of your data folder
         /path/to/your/data/derivatives \ # where you want mriqc output to be saved. As you are running the group level analysis this folder should be prepopulated with the results of the participant level analysis
         group \ # this tells mriqc to agive you the group report
         -w /path/to/work/directory \ #useful to specify so your home directory definitely does not get clogged
         --nprocs 6 --mem_gb 10000 \ # mriqc can be greedy on the hpc, make sure it is not
         -v # be verbal mriqc, tell me what you are doing

Hit enter, and mriqc should now be merrily working away on your data :)

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