slimnsour/dmripreproc

Until we come up with a better name

# <img alt="dmripreproc" src="docs/img/dmripreproc_icon.svg" height="128"> dmripreproc

Preprocessing of neuroimaging data in preparation for AFQ analysis

• Free software: BSD license
• Documentation: https://dmripreproc.readthedocs.io.

## Preparing your data

You should have raw data organized in the BIDS format. Also, you should have run Freesurfer and the results should be in a derivatives/ folder:

BIDS_input_dir ├── sub-01 │   ├── dwi │ │   ├── sub-01_ses-01_dwi.nii.gz │ │   ├── sub-01_ses-01_dwi.bval │ │   ├── sub-01_ses-01_dwi.bvec │   ├── fmap │ │   ├── sub-01_ses-01_acq-dwi_dir-AP_epi.nii.gz │ │   ├── sub-01_ses-01_acq-dwi_dir-PA_epi.nii.gz │ │   ├── sub-01_ses-01_acq-dwi_dir-AP_epi.json │ │   ├── sub-01_ses-01_acq-dwi_dir-PA_epi.json ├── derivatives │   ├── sub-01 │ │   ├── freesurfer

## Quickstart

```bash git clone https://github.com/nipy/dmripreproc cd dmripreproc python setup.py install

dmripreproc $BIDS_INPUT_DIR $OUTPUT_DIR --participant-label 01 ```

```bash git clone https://github.com/nipy/dmripreproc cd dmripreproc make docker

# If you don't want to log into the docker image:

docker run -ti -v $BIDS_INPUT_DIR:/inputs -v $OUTPUT_DIR:/outputs dmripreproc:prod dmripreproc /inputs /outputs

# If you want to log into the image:

docker run -ti -v $BIDS_INPUT_DIR:/inputs -v $OUTPUT_DIR:/outputs dmripreproc:prod

# Run this inside the docker image: dmripreproc /inputs /outpus --participant-label 01 ```

## Features

• TODO

## Contributing

We love contributions! dmripreproc is open source, built on open source, and we'd love to have you hang out in our community.

We have developed some [guidelines](CONTRIBUTING.rst) for contributing to dmripreproc.

Imposter syndrome disclaimer: We want your help. No, really.

There may be a little voice inside your head that is telling you that you're not ready to be an open source contributor; that your skills aren't nearly good enough to contribute. What could you possibly offer a project like this one?

We assure you - the little voice in your head is wrong. If you can write code at all, you can contribute code to open source. Contributing to open source projects is a fantastic way to advance one's coding skills. Writing perfect code isn't the measure of a good developer (that would disqualify all of us!); it's trying to create something, making mistakes, and learning from those mistakes. That's how we all improve, and we are happy to help others learn.

Being an open source contributor doesn't just mean writing code, either. You can help out by writing documentation, tests, or even giving feedback about the project (and yes - that includes giving feedback about the contribution process). Some of these contributions may be the most valuable to the project as a whole, because you're coming to the project with fresh eyes, so you can see the errors and assumptions that seasoned contributors have glossed over.

## Credits

This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [audreyr/cookiecutter-pypackage](https://github.com/audreyr/cookiecutter-pypackage) project template.

The imposter syndrome disclaimer was originally written by [Adrienne Lowe](https://github.com/adriennefriend) for a [PyCon talk](https://www.youtube.com/watch?v=6Uj746j9Heo), and was adapted based on its use in the README file for the [MetPy project](https://github.com/Unidata/MetPy).