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spine-generic / data-multi-subject_DO-NOT-USE

Multi-subject data for the Spine Generic project
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Fix defacing #23

Closed alexfoias closed 4 years ago

alexfoias commented 4 years ago

The issues signalled here: https://github.com/spine-generic/data-multi-subject/pull/21#issuecomment-667390603 Fixes: https://github.com/spine-generic/data-multi-subject/issues/22

Here are the details concerning the file permissions.

``` (base) alfoi@MacBook-Pro:anat % pwd /Users/alfoi/code/data-multi-subject/sub-cmrra02/anat (base) alfoi@MacBook-Pro:anat % ll total 66496 drwxr-xr-x 14 alfoi staff 448 12 Aug 11:19 . drwxr-xr-x 4 alfoi staff 128 12 Aug 09:46 .. -rw-r--r-- 1 alfoi staff 2174 12 Aug 09:46 sub-cmrra02_T1w.json -rw-r--r-- 1 alfoi staff 18582870 12 Aug 09:46 sub-cmrra02_T1w.nii.gz -rw-r--r-- 1 alfoi staff 2324 12 Aug 09:46 sub-cmrra02_T2star.json -rw-r--r-- 1 alfoi staff 2457557 12 Aug 09:46 sub-cmrra02_T2star.nii.gz -rw-r--r-- 1 alfoi staff 2265 12 Aug 09:46 sub-cmrra02_T2w.json -rw-r--r-- 1 alfoi staff 7487369 8 Jul 2019 sub-cmrra02_T2w.nii.gz -rw-r--r-- 1 alfoi staff 2118 12 Aug 09:46 sub-cmrra02_acq-MToff_MTS.json -rw-r--r-- 1 alfoi staff 1832204 12 Aug 09:46 sub-cmrra02_acq-MToff_MTS.nii.gz -rw-r--r-- 1 alfoi staff 2147 12 Aug 09:46 sub-cmrra02_acq-MTon_MTS.json -rw-r--r-- 1 alfoi staff 1803306 12 Aug 09:46 sub-cmrra02_acq-MTon_MTS.nii.gz -rw-r--r-- 1 alfoi staff 2119 12 Aug 09:46 sub-cmrra02_acq-T1w_MTS.json -rw-r--r-- 1 alfoi staff 1847357 12 Aug 09:46 sub-cmrra02_acq-T1w_MTS.nii.gz (base) alfoi@MacBook-Pro:anat % pwd /Users/alfoi/code/data-multi-subject/sub-cmrra04/anat (base) alfoi@MacBook-Pro:anat % ll total 67096 drwxr-xr-x 14 alfoi staff 448 12 Aug 11:20 . drwxr-xr-x 4 alfoi staff 128 12 Aug 09:46 .. -rw-r--r-- 1 alfoi staff 2174 12 Aug 09:46 sub-cmrra04_T1w.json -rw-r--r-- 1 alfoi staff 18771077 12 Aug 09:46 sub-cmrra04_T1w.nii.gz -rw-r--r-- 1 alfoi staff 2330 12 Aug 09:46 sub-cmrra04_T2star.json -rw-r--r-- 1 alfoi staff 2429209 12 Aug 09:46 sub-cmrra04_T2star.nii.gz -rw-r--r-- 1 alfoi staff 2266 12 Aug 09:46 sub-cmrra04_T2w.json -rw-r--r--@ 1 alfoi staff 7894535 11 Aug 16:23 sub-cmrra04_T2w.nii.gz -rw-r--r-- 1 alfoi staff 2121 12 Aug 09:46 sub-cmrra04_acq-MToff_MTS.json -rw-r--r-- 1 alfoi staff 1734866 12 Aug 09:46 sub-cmrra04_acq-MToff_MTS.nii.gz -rw-r--r-- 1 alfoi staff 2150 12 Aug 09:46 sub-cmrra04_acq-MTon_MTS.json -rw-r--r-- 1 alfoi staff 1730969 12 Aug 09:46 sub-cmrra04_acq-MTon_MTS.nii.gz -rw-r--r-- 1 alfoi staff 2121 12 Aug 09:46 sub-cmrra04_acq-T1w_MTS.json -rw-r--r-- 1 alfoi staff 1756789 12 Aug 09:46 sub-cmrra04_acq-T1w_MTS.nii.gz (base) alfoi@MacBook-Pro:anat % pwd /Users/alfoi/code/data-multi-subject/sub-cmrra05/anat (base) alfoi@MacBook-Pro:anat % ll total 66696 drwxr-xr-x 14 alfoi staff 448 12 Aug 11:20 . drwxr-xr-x 4 alfoi staff 128 12 Aug 09:46 .. -rw-r--r-- 1 alfoi staff 2175 12 Aug 09:46 sub-cmrra05_T1w.json -rw-r--r-- 1 alfoi staff 18276616 12 Aug 09:46 sub-cmrra05_T1w.nii.gz -rw-r--r-- 1 alfoi staff 2332 12 Aug 09:46 sub-cmrra05_T2star.json -rw-r--r-- 1 alfoi staff 2484240 12 Aug 09:46 sub-cmrra05_T2star.nii.gz -rw-r--r-- 1 alfoi staff 2261 12 Aug 09:46 sub-cmrra05_T2w.json -rw-r--r--@ 1 alfoi staff 8091670 11 Aug 16:29 sub-cmrra05_T2w.nii.gz -rw-r--r-- 1 alfoi staff 2122 12 Aug 09:46 sub-cmrra05_acq-MToff_MTS.json -rw-r--r-- 1 alfoi staff 1787358 12 Aug 09:46 sub-cmrra05_acq-MToff_MTS.nii.gz -rw-r--r-- 1 alfoi staff 2150 12 Aug 09:46 sub-cmrra05_acq-MTon_MTS.json -rw-r--r-- 1 alfoi staff 1726570 12 Aug 09:46 sub-cmrra05_acq-MTon_MTS.nii.gz -rw-r--r-- 1 alfoi staff 2121 12 Aug 09:46 sub-cmrra05_acq-T1w_MTS.json -rw-r--r-- 1 alfoi staff 1741365 12 Aug 09:46 sub-cmrra05_acq-T1w_MTS.nii.gz (base) alfoi@MacBook-Pro:anat % pwd /Users/alfoi/code/data-multi-subject/sub-oxfordFmrib07/anat (base) alfoi@MacBook-Pro:anat % ll total 67000 drwxr-xr-x 14 alfoi staff 448 12 Aug 12:06 . drwxr-xr-x 4 alfoi staff 128 12 Aug 09:46 .. -rw-r--r-- 1 alfoi staff 1672 12 Aug 09:46 sub-oxfordFmrib07_T1w.json -rw-r--r--@ 1 alfoi staff 15613969 12 Aug 12:07 sub-oxfordFmrib07_T1w.nii.gz -rw-r--r-- 1 alfoi staff 1775 12 Aug 09:46 sub-oxfordFmrib07_T2star.json -rw-r--r-- 1 alfoi staff 2599366 12 Aug 09:46 sub-oxfordFmrib07_T2star.nii.gz -rw-r--r-- 1 alfoi staff 1718 12 Aug 09:46 sub-oxfordFmrib07_T2w.json -rw-r--r-- 1 alfoi staff 10072546 12 Aug 09:46 sub-oxfordFmrib07_T2w.nii.gz -rw-r--r-- 1 alfoi staff 1624 12 Aug 09:46 sub-oxfordFmrib07_acq-MToff_MTS.json -rw-r--r-- 1 alfoi staff 1931051 12 Aug 09:46 sub-oxfordFmrib07_acq-MToff_MTS.nii.gz -rw-r--r-- 1 alfoi staff 1647 12 Aug 09:46 sub-oxfordFmrib07_acq-MTon_MTS.json -rw-r--r-- 1 alfoi staff 1946663 12 Aug 09:46 sub-oxfordFmrib07_acq-MTon_MTS.nii.gz -rw-r--r-- 1 alfoi staff 1623 12 Aug 09:46 sub-oxfordFmrib07_acq-T1w_MTS.json -rw-r--r-- 1 alfoi staff 1922610 12 Aug 09:46 sub-oxfordFmrib07_acq-T1w_MTS.nii.gz (base) alfoi@MacBook-Pro:anat % pwd /Users/alfoi/code/data-multi-subject/sub-dresden02/anat (base) alfoi@MacBook-Pro:anat % ll total 73720 drwxr-xr-x 14 alfoi staff 448 12 Aug 09:46 . drwxr-xr-x 4 alfoi staff 128 12 Aug 09:46 .. -rw-r--r-- 1 alfoi staff 1813 12 Aug 09:46 sub-dresden02_T1w.json -rw-r--r-- 1 alfoi staff 18644946 12 Aug 09:46 sub-dresden02_T1w.nii.gz -rw-r--r-- 1 alfoi staff 2307 12 Aug 09:46 sub-dresden02_T2star.json -rw-r--r-- 1 alfoi staff 2873815 12 Aug 09:46 sub-dresden02_T2star.nii.gz -rw-r--r-- 1 alfoi staff 2302 12 Aug 09:46 sub-dresden02_T2w.json -rw-r--r--@ 1 alfoi staff 10268093 12 Aug 11:22 sub-dresden02_T2w.nii.gz -rw-r--r-- 1 alfoi staff 2122 12 Aug 09:46 sub-dresden02_acq-MToff_MTS.json -rw-r--r-- 1 alfoi staff 1890910 12 Aug 09:46 sub-dresden02_acq-MToff_MTS.nii.gz -rw-r--r-- 1 alfoi staff 2150 12 Aug 09:46 sub-dresden02_acq-MTon_MTS.json -rw-r--r-- 1 alfoi staff 1862390 12 Aug 09:46 sub-dresden02_acq-MTon_MTS.nii.gz -rw-r--r-- 1 alfoi staff 2123 12 Aug 09:46 sub-dresden02_acq-T1w_MTS.json -rw-r--r-- 1 alfoi staff 1891286 12 Aug 09:46 sub-dresden02_acq-T1w_MTS.nii.gz (base) alfoi@MacBook-Pro:anat % pwd /Users/alfoi/code/data-multi-subject/sub-stanford06/anat (base) alfoi@MacBook-Pro:anat % ll total 67456 drwxr-xr-x 14 alfoi staff 448 12 Aug 11:41 . drwxr-xr-x 5 alfoi staff 160 12 Aug 11:30 .. -rw-r--r-- 1 alfoi staff 1189 12 Aug 09:46 sub-stanford06_T1w.json -rw-r--r-- 1 alfoi staff 19674534 12 Aug 11:31 sub-stanford06_T1w.nii.gz -rw-r--r-- 1 alfoi staff 1206 12 Aug 09:46 sub-stanford06_T2star.json -rw-r--r-- 1 alfoi staff 3166887 12 Aug 09:46 sub-stanford06_T2star.nii.gz -rw-r--r-- 1 alfoi staff 1193 12 Aug 09:46 sub-stanford06_T2w.json -rw-r--r-- 1 alfoi staff 7826733 12 Aug 09:46 sub-stanford06_T2w.nii.gz -rw-r--r-- 1 alfoi staff 1153 12 Aug 09:46 sub-stanford06_acq-MToff_MTS.json -rw-r--r-- 1 alfoi staff 1230228 12 Aug 09:46 sub-stanford06_acq-MToff_MTS.nii.gz -rw-r--r-- 1 alfoi staff 1159 12 Aug 09:46 sub-stanford06_acq-MTon_MTS.json -rw-r--r-- 1 alfoi staff 1128568 12 Aug 09:46 sub-stanford06_acq-MTon_MTS.nii.gz -rw-r--r-- 1 alfoi staff 1154 12 Aug 09:46 sub-stanford06_acq-T1w_MTS.json -rw-r--r-- 1 alfoi staff 1162567 12 Aug 09:46 sub-stanford06_acq-T1w_MTS.nii.gz ```
jcohenadad commented 4 years ago

@kousu ok to continue opening PR here or should we move to the new git-annex?

kousu commented 4 years ago

Sorry, but after #20, can you re-submit this over at the new https://github.com/spine-generic/data-multi-subject ?

Because this PR touched NifTis, it's going to need more steps than #26 to integrate. It might be easiest if you just started fresh:

  1. Get #26 and #27 merged first.
  2. Rename https://github.com/alexfoias/data-multi-subject to https://github.com/alexfoias/data-multi-subject_DO-NOT-USE.
  3. Re-fork https://github.com/spine-generic/data-multi-subject to https://github.com/alexfoias/data-multi-subject.
  4. Reapply your work:
mv data-multi-subject data-multi-subject_DO-NOT-USE

git clone git@github.com:alexfoias/data-multi-subject.git
cd data-multi-subject
git annex init

# re-integrate changes
git checkout -b fix_defacing
git annex get sub-cmrra02  sub-cmrra04 sub-cmrra05 sub-oxfordFmrib07 sub-dresden02 sub-stanford06
cp -rp ../data-multi-subject_DO-NOT-USE/{sub-cmrra02,sub-cmrra04,sub-cmrra05,sub-oxfordFmrib07,sub-dresden02,sub-stanford06} .
git add -u  # this will hang for a moment as git-annex indexes the new files
git commit

Then to upload your work, follow https://github.com/kousu/data-multi-subject/blob/git-annex-docs/CONTRIBUTING.md. In particular, @jcohenadad has to make you a key for Amazon. With that in hand, do:

export AWS_ACCESS_KEY_ID="..." AWS_SECRET_ACCESS_KEY="..."
git annex sync --content

This will tell you it's uploading the NifTis to Amazon and the rest to Github. If not, try the more explicit version on CONTRIBUTING.md.

Then you should be able to re-create the pull request from the new branch.

I'm sorry about all this. Migrations are painful.

jcohenadad commented 4 years ago

This PR has now been ported to https://github.com/spine-generic/data-multi-subject/pull/19