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bids-apps / mindboggle

Improve the accuracy, precision, and consistency of automated labeling and shape analysis of human brain image data
Apache License 2.0
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bids bidsapp mri

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mindboggle

Build Status

Description

The Mindboggle project's mission is to improve the accuracy, precision, and consistency of automated labeling and shape analysis of human brain image data. We promote open science by making all software, data, and documentation freely and openly available. For more information on mindboggle, check out the mindboggle website

Docker

To pull the docker image from Docker Hub, do

docker pull bids/mindboggle

To run the docker, do:

docker run -ti \
    -v $PWD/ds114_test1:/home/jovyan/work/data \
    bids/mindboggle \
        /home/jovyan/work/data \
        /home/jovyan/work/data/derivatives/ participant

Its important to mount to a directory in /home/jovyan/ because you are not root in this Docker image.

To use bash:

 docker run -ti \
    -v /Users/keshavan/Downloads/mindboggle_input_example/bids:/home/jovyan/work/data \
    --entrypoint /bin/bash \
        bids/mindboggle

For developers, you can make changes to the Dockerfile, and build the docker image, by running

docker build -t bids/mindboggle .

Acknowledgements

When using this app, please cite:

101 labeled brain images and a consistent human cortical labeling protocol.
Arno Klein, Jason Tourville. 2012. Frontiers in Brain Imaging Methods.
6:171. DOI: 10.3389/fnins.2012.00171

Error Reporting

Please report errors on the Issues page of this repository.