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SpineGenericSingleDataset

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# Spine Generic Public Database (Single Subject)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4299148.svg)](https://doi.org/10.5281/zenodo.4299148)
[![BIDS Validator](https://github.com/spine-generic/data-single-subject/workflows/BIDS%20Validator/badge.svg)](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 🎉 

	a/README.md		b/README.md
1	# Spine Generic Public Database (Single Subject)	1	# Spine Generic Public Database (Single Subject)
2	[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4299148.svg)](https://doi.org/10.5281/zenodo.4299148)	2	[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4299148.svg)](https://doi.org/10.5281/zenodo.4299148)
3	[![BIDS Validator](https://github.com/spine-generic/data-single-subject/workflows/BIDS%20Validator/badge.svg)](https://github.com/spine-generic/data-single-subject/actions?query=workflow%3A%22BIDS+Validator%22)	3	[![BIDS Validator](https://github.com/spine-generic/data-single-subject/workflows/BIDS%20Validator/badge.svg)](https://github.com/spine-generic/data-single-subject/actions?query=workflow%3A%22BIDS+Validator%22)
4		4
5	## About this dataset	5	## About this dataset
6		6
7	This dataset was acquired using the [spine-generic protocol](http://spinalcordmri.org/protocols)	7	This dataset was acquired using the [spine-generic protocol](http://spinalcordmri.org/protocols)
8	on a 38 y.o. male healthy subject. The list of sites is available in [participants.tsv](./participants.tsv).	8	on a 38 y.o. male healthy subject. The list of sites is available in [participants.tsv](./participants.tsv).
9		9
10	This dataset follows the [BIDS](https://bids.neuroimaging.io/) convention.	10	This dataset follows the [BIDS](https://bids.neuroimaging.io/) convention.
11		11
12	The contributor has the necessary ethics & permissions to share the data publicly.	12	The contributor has the necessary ethics & permissions to share the data publicly.
13		13
14	The dataset does not include any identifiable personal health information, including names,	14	The dataset does not include any identifiable personal health information, including names,
15	zip codes, dates of birth, facial features on structural scans.	15	zip codes, dates of birth, facial features on structural scans.
16		16
17	The entire dataset is about 1GB.	17	The entire dataset is about 1GB.
18		18
19	## Download	19	## Download
20		20
21	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:	21	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:
22		22
23	~~~	23	~~~
24	git clone https://github.com/spine-generic/data-single-subject && \	24	git clone https://github.com/spine-generic/data-single-subject && \
25	cd data-single-subject && \	25	cd data-single-subject && \
26	git annex init && \	26	git annex init && \
27	git annex get	27	git annex get
28	~~~	28	~~~
29		29
30	You may substitute `git annex get` with more specific commands if you are only interested in certain subjects. For example:	30	You may substitute `git annex get` with more specific commands if you are only interested in certain subjects. For example:
31		31
32	```	32	```
33	git annex get sub-douglas sub-juntendoPrisma/anat/	33	git annex get sub-douglas sub-juntendoPrisma/anat/
34	```	34	```
35		35
36	## Working from a forked repository	36	## Working from a forked repository
37		37
38	> ⚠️ For advanced users only. Normally the instructions under [Download](#Download) should be enough.	38	⚠️ For advanced users only. Normally the instructions under [Download](#Download) should be enough.
39	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:	39	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:
40	```	40	```
41	get some-file-name.nii.gz (not available)	41	get some-file-name.nii.gz (not available)
42	No other repository is known to contain the file.	42	No other repository is known to contain the file.
43	(Note that these git remotes have annex-ignore set: origin)	43	(Note that these git remotes have annex-ignore set: origin)
44	failed	44	failed
45	```	45	```
46		46
47	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:	47	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:
48	```	48	```
49	git remote -v	49	git remote -v
50	# the answer should show both your-user-name/data-single-subject.git (probably named "origin")	50	# the answer should show both your-user-name/data-single-subject.git (probably named "origin")
51	# and spine-generic/data-single-subject (probably named "upstream")	51	# and spine-generic/data-single-subject (probably named "upstream")
52	```	52	```
53		53
54	If `spine-generic/data-single-subject` is missing, you can add it with:	54	If `spine-generic/data-single-subject` is missing, you can add it with:
55	```	55	```
56	git remote add upstream https://github.com/spine-generic/data-single-subject.git	56	git remote add upstream https://github.com/spine-generic/data-single-subject.git
57	git config remote.upstream.annex-readonly true	57	git config remote.upstream.annex-readonly true
58	```	58	```
59		59
60	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`:	60	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`:
61	```	61	```
62	git fetch upstream +refs/heads/git-annex:refs/remotes/upstream/git-annex	62	git fetch upstream +refs/heads/git-annex:refs/remotes/upstream/git-annex
63	git pull && git annex get .	63	git pull && git annex get .
64	```	64	```
65		65
66	## Analysis	66	## Analysis
67		67
68	The instructions to process this dataset are available in the [spine-generic documentation](https://spine-generic.readthedocs.io/en/latest/analysis-pipeline.html).	68	The instructions to process this dataset are available in the [spine-generic documentation](https://spine-generic.readthedocs.io/en/latest/analysis-pipeline.html).
69		69
70	## Contributing	70	## Contributing
71		71
72	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 🎉	72	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 🎉