Using mriqc with neurodesk on HPC

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.

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:

Open MRIQC

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

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

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

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 :)