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Fix defacing #23

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Fix defacing #23

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alexfoias
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@alexfoias alexfoias commented Aug 12, 2020 •
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The issues signalled here: spine-generic/data-multi-subject#21 (comment)
Fixes: spine-generic/data-multi-subject#22

  • sub-cmrra02: fixed T2w
    Untitled 001
  • sub-cmrra04: fixed T2w
    Untitled 002
  • sub-cmrra05 : fixed T2w
    Untitled 003
  • sub-oxfordFmrib07: fixed T1w
    Screen Shot 2020-08-12 at 12 11 10 PM
  • sub-dresden02: fixed T2w
    Untitled 004
  • sub-stanford06: fixed T1w
    Untitled 005

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 and others added 30 commits June 30, 2020 16:31
@jcohenadad
Added sub-amu -> sub-barcelona
1994954
@jcohenadad
Added sub-beijing -> sub-brnoUhb
20c3b45
@jcohenadad
Added sub-beijingGE, resampled anat/*T1w to 1x1x1mm
18de912 
To fit <100MB github requirement
@jcohenadad
Updated README
ee5c343
@jcohenadad
Fixed title
352dfd1
@jcohenadad
Added sub-cardiff -> sub-hamburg
f9f25f3
@jcohenadad
Added sub-juntendo750w -> sub-nwu
b337781
@jcohenadad
Added sub-oxfordFmrib -> sub-perform06/dwi/sub-perform
5d1fc38
@jcohenadad
Added sub-queensland -> sub-strasbourg
54278f6
@jcohenadad
Added sub-tehran -> sub-tokyoSkyra
a45add5
@jcohenadad
Added sub-ubc -> sub-unf
8b8ad89
@jcohenadad
Added sub-vallHebron -> sub-vuissIngenia
fe34650
@jcohenadad
Fixed Bath -> Barth
a312047
@jcohenadad
Added .gitignore
3a06c6f
@jcohenadad
Merge branch 'master' of github.com:spine-generic/data-multi-subject
e679893
@jcohenadad
Update README.md
a5146f7
@jcohenadad
Update README.md
3d7967e
@charleygros
add csf masks
f4ea9db
@charleygros
Merge pull request #5 from spine-generic/cg/csf_masks
6ce68c0 
derivatives/labels folder and csfseg-manual masks
@jcohenadad
Added manual labels
bc7b8de
@jcohenadad
Fixed broken link
8f355d7
@alexfoias
fix participants.tsv
2b89166
@jcohenadad
Merge pull request #11 from alexfoias/master
7d707ee 
Fix wrong acquisition date in participants.tsv
@alexfoias
add travis
e13d80c
@alexfoias
add badge
7dd70dd
@alexfoias
add bids ignore
9d37346
@jcohenadad
Merge pull request #12 from alexfoias/master
f96d408 
Implement CI testing for BIDS
@jcohenadad
Removed old manual corrections
294c7b3 
Fixes #8
@valosekj
Add files via upload
c900a87 
Add manually corrected dwi SC segmentations.
@valosekj
Add files via upload
75c2bdb 
Update dwi SC seg for sub-vuiisAchieva06
jcohenadad and others added 8 commits July 30, 2020 07:10
@jcohenadad
Merge pull request #15 from valosekj/master
5b09469 
Add manually corrected dwi SC segmentations
@PaulBautin
- manual correction of t1w and t2w images
a3776b3
@PaulBautin
- labeling correction click inside the spinal cord
b25b78d
@PaulBautin
- remove cmrra02
d8b444f 
- remove sapienza04 gmseg
- correct gmseg for sapienza01
@jcohenadad
Merge pull request #16 from PaulBautin/pb_corrections_t1w_t2w
b00b64b 
manual correction of t1w and t2w images
@alexfoias
Add dataset fslAchieva & fslPrisma (#21)
8d08c11 
* fix defaced image

* change permissions

* add fslPrisma dataset

* rename sapienza to fslAchieva

* deface images

* fix defacing dresden02_T2w

* remove other defaced images

* rename test

* fix rename
@alexfoias
Fix defacing
ba2e5f5
@alexfoias
fix defacing
4abc8b2
@jcohenadad
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@kousu ok to continue opening PR here or should we move to the new git-annex?

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kousu commented Aug 13, 2020 •
edited
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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 Fix participants.tsv #26 and implement CI check_data_consistency #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 [email protected]: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.

This was referenced Aug 27, 2020
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@jcohenadad
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This PR has now been ported to spine-generic/data-multi-subject#19

@jcohenadad jcohenadad closed this Aug 27, 2020
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6 participants
@alexfoias @jcohenadad @kousu @charleygros @valosekj @PaulBautin