README.md

# HW3: mriqc

Due 3/2.

# Overview

Use mriqc and singularity to prepare quality control reports for the sample dataset at `/scratch/psyc5171/exercises/mbdata/bids`.

# Dataset

The dataset for this and subsequent pipeline demos is adapted from [ds001544](https://openneuro.org/datasets/ds001544/versions/1.1.0) and contains a single subject and session with T1w, T2w, bold/sbref, and epi fieldmap modalities. Note that the scans have been renamed from the original dataset and some of the metadata has been modified.

# Exercise

1. Fork and clone this repository to the cluster.
2. Edit the `sbatch_mriqc.sh` script to run mriqc
3. Submit your job
4. When mriqc has successfully run, use git to add, commit, push, and pull request.


# Notes

The minimal mriqc command is:

```bash
singularity run --cleanenv \
--bind ${BIDS_DIR}:/data \
--bind ${OUT_DIR}:/out \
/scratch/psyc5171/containers/mriqc_latest.sif \
/data /out participant
```


You need to provide two directories for this to work:

- `${BIDS_DIR}` is the full path to the BIDS folder. Since mriqc does not modify the input BIDS folder, you do not need to copy the input data to your own directory. 
- `${OUT_DIR}` is the full path to a directory where the output files will go. This directory needs to be under your control and exist prior to running mriqc (use `mkdir` to create a new directory). For example, you might create the directory `/scratch/${USER}/hw3/mriqc` to store the output, and would replace the string `${OUT_DIR}` with this path, so the line would read `--bind /scratch/${USER}/hw3/mriqc:/out`.
- The command above needs to be in a SLURM script. You can adapt a script from your previous homework as a starting point. Don't forget to include the `module load singularity` command in your SLURM script.
- See the slides for notes on resource needs. If you adjust the mriqc `--nprocs` option to use 2 or 3 processors, the script should not take more than 1 hour to run.

# git workarounds

- To associate your clone with your GitHub username, run the command

	```bash
	git remote set-url origin \
	https://${USER}@github.uconn.edu/${USER}/hw3.git
	```
	in your `hw3` directory. This will avoid the `The requested URL 	returned error: 403 Forbidden while accessing ` error when pushing.
- Use the command `unset SSH_ASKPASS` prior to pushing to avoid the error `(gnome-ssh-askpass:19484): Gtk-WARNING **: cannot open display:`
- When committing, you can specify a short commit message on the command line with the `-m` option: `git commit -m 'commit message'`. If you do not do this, the default editor will open so you can write your commit message. The default is usually `vi`.
	- Press `i` to enter insertion mode and write your message
	- Press `ctrl-c` or `esc` to exit insertion mode
	- Type `:wq` to save and quit or `:q!` to quite without saving

- The command `git status` will show files that have changed since the last commit.
- The command `git log` will show the commit history

# Resources

- The [BIRC computing guide](https://bircibrain.github.io/computingguide/docs/fmri-preprocessing/mriqc.html) has some more detailed instructions on running mriqc. The guide also provides instructions for downloading the container image, but this has already been done for you.
- The [mriqc](https://mriqc.readthedocs.io/en/stable/) webpage has additional documentation on the various options, and more detailed descriptions and references for the quality metrics.

 
# Troubleshooting

- Consult your sbatch log files for clues to the cause of errors, e.g. missing files.
- It is sometimes neccessary to remove partial outputs from your mriqc output directory in order to successfully rerun the pipeline.
-  mriqc and many other BIDS Apps will create a `work` directory that stores temporary files. It can be helpful to also remove this directory before rerunning a failed mriqc job.
-  Files can be deleted with the `rm` command. Directories (and the directories/files they contain) can be removed with `rm -r`. Make sure you know what you are deleting before running this command!