---
title: "Using mriqc with neurodesk on HPC"
linkTitle: "mriqc"
weight: 1
tags: ["mriqc", "documentation", "preprocessing"]
author: Kelly G. Garner
aliases:
- /tutorials/functional_imaging/mriqc_cvl
- /tutorials-examples/tutorials/functional_imaging/mriqc_cvl
description: > 
  A brief guide to using mriqc with neurodesk.
---

# 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](https://github.com/garner-code)
>

> 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. 

<!-- Following line adds a link to getting set up with Neurodesk -->
[Getting Set Up with Neurodesk](https://neurodesk.org/getting-started/)
<!-- -->

---

## Assumptions

- [ ] Your data is already in [BIDS format](https://bids.neuroimaging.io/)
- [ ] 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](/static/tutorials/functional_imaging/mriqc/launch_neurodesk.png 'launch_neurodesk') <!-- ![filename without extension](/subfolder_name/filename.png '[filename without extension')  -->

### Open MRIQC

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

![neurodesk_menu](/static/tutorials/functional_imaging/mriqc/neurodesk_menu.png 'neurodesk_menu') <!-- ![filename without extension](/subfolder_name/filename.png '[filename without extension')  -->

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

![open_mriqc](/static/tutorials/functional_imaging/mriqc/open_mriqc.png 'open_mriqc') <!-- ![filename without extension](/subfolder_name/filename.png '[filename without extension')  -->

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

![mriqc_bash](/static/tutorials/functional_imaging/mriqc/mriqc_bash.png 'mriqc_bash') <!-- ![filename without extension](/subfolder_name/filename.png '[filename without extension')  -->

### Setting up mriqc command

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

```go

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 :)