Spine Generic Public Database (Single Subject)

About this dataset

This dataset was acquired using the spine-generic protocol on a 38 y.o. male healthy subject. The list of sites is available in participants.tsv.

This dataset follows the BIDS convention.

The contributor has 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 1GB.

Download

We are using a tool to manage large datasets called git-annex. To download, dataset, you need to have git installed, and also install git-annex of version 8. Then run:

git clone https://github.com/spine-generic/data-single-subject && \
cd data-single-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-douglas sub-juntendoPrisma/anat/

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-single-subject of spine-generic/data-single-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-single-subject, make sure that spine-generic/data-single-subject is also configured as a remote:

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

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

   git remote add upstream https://github.com/spine-generic/data-single-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-single-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.

Contributing

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