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--- a/README.md +++ b/README.md @@ -1,96 +1,94 @@ -# Spine Generic Public Database (Multi-Subject) -[](https://doi.org/10.5281/zenodo.4299140) -[](https://github.com/spine-generic/data-multi-subject/actions?query=workflow%3A%22Dataset+Validator%22) - -## About this dataset - -This dataset was acquired using the [spine-generic protocol](http://spinalcordmri.org/protocols) -on multiple subjects, multiple sites and multiple MRI vendors and models. The list of subjects -is available in [participants.tsv](./participants.tsv). - -This dataset follows the [BIDS](https://bids.neuroimaging.io/) 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 **26GB**. - -## 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`](https://github.com/neuropoly/data-management/blob/master/git-annex.md#installation) - -> ⚠️ 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](https://git-annex.branchable.com/walkthrough/) and take note of our [in-lab troubleshooting](https://github.com/neuropoly/data-management/blob/master/git-annex.md). - -## Working from a forked repository - -> ⚠️ For advanced users only. Normally the instructions under [Download](#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](https://spine-generic.readthedocs.io/en/latest/analysis-pipeline.html). - -## Help - -If you have problems downloading the dataset, please post an [issue](https://github.com/spine-generic/data-multi-subject/issues). 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](https://github.com/spine-generic/spine-generic/wiki/git-annex). Thank you for your contribution 🎉 +# Spine Generic Public Database (Multi-Subject) +[](https://doi.org/10.5281/zenodo.4299140) +[](https://github.com/spine-generic/data-multi-subject/actions?query=workflow%3A%22Dataset+Validator%22?raw=true) + +## About this dataset + +This dataset was acquired using the [spine-generic protocol](http://spinalcordmri.org/protocols) +on multiple subjects, multiple sites and multiple MRI vendors and models. The list of subjects +is available in [participants.tsv](./participants.tsv). + +This dataset follows the [BIDS](https://bids.neuroimaging.io/) 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 **26GB**. + +## 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`](https://github.com/neuropoly/data-management/blob/master/git-annex.md#installation) + +> ⚠️ 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](https://git-annex.branchable.com/walkthrough/) and take note of our [in-lab troubleshooting](https://github.com/neuropoly/data-management/blob/master/git-annex.md). + +## Working from a forked repository + +###⚠️ For advanced users only. Normally the instructions under [Download](#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](https://spine-generic.readthedocs.io/en/latest/analysis-pipeline.html). + +## Help + +If you have problems downloading the dataset, please post an [issue](https://github.com/spine-generic/data-multi-subject/issues). 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](https://github.com/spine-generic/spine-generic/wiki/git-annex). Thank you for your contribution 🎉