Skip to content
preprocessing for dMRI data
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
.github
dmriprep
dmriprepViewer
docker
docs
kubernetes
tests
.editorconfig
.gitignore
.travis.yml
AUTHORS.rst
CONTRIBUTING.rst Rename all preafq stuff to dmriprep. Nov 21, 2018
Dockerfile-dmriprep
HISTORY.rst
LICENSE
MANIFEST.in
Makefile
README.rst
requirements_dev.txt
setup.cfg
setup.py
tox.ini

README.rst

dmriprep

Documentation Status

Preprocessing of neuroimaging data in preparation for AFQ analysis

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 | |-- derivatives | |-- sub-01 | |-- freesurfer `

Quickstart

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

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

Features

  • TODO

Contributing

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

We have developed some guidelines for contributing to dmriprep.

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 and the audreyr/cookiecutter-pypackage project template.

The imposter syndrome disclaimer was originally written by Adrienne Lowe for a `PyCon talk`_, and was adapted based on its use in the README file for the MetPy project.

You can’t perform that action at this time.