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spine-generic / data-multi-subject

Multi-subject data for the Spine Generic project
Creative Commons Attribution 4.0 International
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Spine Generic Public Database (Multi-Subject)

DOI BIDS Validator

About this dataset

This dataset was acquired using the spine-generic protocol on multiple subjects, multiple sites and multiple MRI vendors and models. The list of subjects is available in participants.tsv.

This dataset follows the BIDS convention. The contributors have the necessary ethics & permissions to share the data publicly.

The dataset does not include any identifiable personal health information, including names, zip codes, dates of birth, facial features on structural scans.

The entire dataset is about 10GB.

Download

We are using a tool to manage large datasets called git-annex. To download this dataset, you need to have git installed, and also install git-annex

⚠️ Make sure you have at least version 8 by running:

git annex version | head -n 1
# the answer should show something like: git-annex version: 8.20200330

Then this will download the dataset:

git clone https://github.com/spine-generic/data-multi-subject && \
cd data-multi-subject && \
git annex init && \
git annex get .

You may substitute git annex get with more specific commands if you are only interested in certain subjects. For example:

git annex get sub-nwu01/ sub-nwu03/ sub-nwu04/ sub-oxfordFmrib04/ sub-tokyoSkyra*/

If you with to update an already-cloned repository, run:

git pull && git annex get .

See more at the official documentation and take note of our in-lab troubleshooting.

Working from a forked repository

⚠️ For advanced users only. Normally the instructions under Download should be enough.

If you have forked this repository on Github (so that you have a copy your-user-name/data-multi-subject of spine-generic/data-multi-subject), you will need to take a few extra synchronization steps to get the latest data with git annex get. Otherwise, you may get an error message like:

get some-file-name.nii.gz (not available)
  No other repository is known to contain the file.

  (Note that these git remotes have annex-ignore set: origin)
failed

  1. In your local clone of your-user-name/data-multi-subject, make sure that spine-generic/data-multi-subject is also configured as a remote:

    git remote -v
# the answer should show both your-user-name/data-multi-subject.git (probably named "origin")
# and spine-generic/data-multi-subject (probably named "upstream")

    If spine-generic/data-multi-subject is missing, you can add it with:

    git remote add upstream https://github.com/spine-generic/data-multi-subject.git
git config remote.upstream.annex-readonly true

  2. Then, to update your local clone, make sure to fetch the git-annex branch from spine-generic/data-multi-subject before running git annex get:

    git fetch upstream +refs/heads/git-annex:refs/remotes/upstream/git-annex
git pull && git annex get .

Analysis

The instructions to process this dataset are available in the spine-generic documentation.

Help

If you have problems downloading the dataset, please post an issue. Document your steps as much as possible and copy/paste the content of your Terminal.

Contributing

If you wish to contribute to this dataset please see the wiki. Thank you for your contribution 🎉