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--- a/README.md +++ b/README.md @@ -1,72 +1,72 @@ -# Spine Generic Public Database (Single Subject) -[](https://doi.org/10.5281/zenodo.4299148) -[](https://github.com/spine-generic/data-single-subject/actions?query=workflow%3A%22BIDS+Validator%22) - -## About this dataset - -This dataset was acquired using the [spine-generic protocol](http://spinalcordmri.org/protocols) -on a 38 y.o. male healthy subject. The list of sites is available in [participants.tsv](./participants.tsv). - -This dataset follows the [BIDS](https://bids.neuroimaging.io/) 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`](https://git-annex.branchable.com/install/) *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](#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](https://spine-generic.readthedocs.io/en/latest/analysis-pipeline.html). - -## 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 (Single Subject) +[](https://doi.org/10.5281/zenodo.4299148) +[](https://github.com/spine-generic/data-single-subject/actions?query=workflow%3A%22BIDS+Validator%22) + +## About this dataset + +This dataset was acquired using the [spine-generic protocol](http://spinalcordmri.org/protocols) +on a 38 y.o. male healthy subject. The list of sites is available in [participants.tsv](./participants.tsv). + +This dataset follows the [BIDS](https://bids.neuroimaging.io/) 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`](https://git-annex.branchable.com/install/) *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](#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](https://spine-generic.readthedocs.io/en/latest/analysis-pipeline.html). + +## 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 🎉