https://github.com/bids-apps/mindboggle

Improve the accuracy, precision, and consistency of automated labeling and shape analysis of human brain image data
https://github.com/bids-apps/mindboggle

bids bidsapp mri

Last synced: about 2 months ago
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Improve the accuracy, precision, and consistency of automated labeling and shape analysis of human brain image data

• Host: GitHub
• URL: https://github.com/bids-apps/mindboggle
• Owner: bids-apps
• License: apache-2.0
• Created: 2016-08-02T20:59:32.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2024-04-30T09:45:51.000Z (5 months ago)
• Last Synced: 2024-06-21T07:18:55.733Z (3 months ago)
• Topics: bids, bidsapp, mri
• Language: Python
• Homepage:
• Size: 62.5 KB
• Stars: 3
• Watchers: 5
• Forks: 4
• Open Issues: 10
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• awesome-bids - mindboggle

README

        
# mindboggle

[![Build Status](https://circleci.com/gh/BIDS-Apps/mindboggle.png?circle-token=:d4d232bd9d9bcf925155774e1b2d24cdc365bd19)](https://circleci.com/gh/BIDS-Apps/mindboggle)

## 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](http://mindboggle.readthedocs.io/en/latest/#preprocessing)

## Docker

To pull the docker image from Docker Hub, do

```bash

docker pull bids/mindboggle

```

To run the docker, do:

```bash

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:

```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

```bash

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.