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neuropoly / intranet.neuro.polymtl.ca

NeuroPoly's lab manual
https://intranet.neuro.polymtl.ca
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Documentation for uploading data in git-annex branch #39

Open jcohenadad opened 2 years ago

jcohenadad commented 2 years ago

I have following this documentation, but I am getting an error at the last step (git push):

Terminal output ```console julien-macbook:~/data.neuro/basel-mp2rage $ git add . julien-macbook:~/data.neuro/basel-mp2rage $ gs A derivatives/labels/sub-P002/anat/sub-P002_UNIT1_seg-manual.json A derivatives/labels/sub-P002/anat/sub-P002_UNIT1_seg-manual.nii.gz A derivatives/labels/sub-P005/anat/sub-P005_UNIT1_seg-manual.json A derivatives/labels/sub-P005/anat/sub-P005_UNIT1_seg-manual.nii.gz A derivatives/labels/sub-P007/anat/sub-P007_UNIT1_seg-manual.json A derivatives/labels/sub-P007/anat/sub-P007_UNIT1_seg-manual.nii.gz A derivatives/labels/sub-P013/anat/sub-P013_UNIT1_seg-manual.json A derivatives/labels/sub-P013/anat/sub-P013_UNIT1_seg-manual.nii.gz A derivatives/labels/sub-P024/anat/sub-P024_UNIT1_seg-manual.json A derivatives/labels/sub-P024/anat/sub-P024_UNIT1_seg-manual.nii.gz A derivatives/labels/sub-P033/anat/sub-P033_UNIT1_seg-manual.json A derivatives/labels/sub-P033/anat/sub-P033_UNIT1_seg-manual.nii.gz A derivatives/labels/sub-P034/anat/sub-P034_UNIT1_seg-manual.json A derivatives/labels/sub-P034/anat/sub-P034_UNIT1_seg-manual.nii.gz A derivatives/labels/sub-P035/anat/sub-P035_UNIT1_seg-manual.json A derivatives/labels/sub-P035/anat/sub-P035_UNIT1_seg-manual.nii.gz julien-macbook:~/data.neuro/basel-mp2rage $ gc [jca/corrected-segs 67e5cee] Added spinal cord manual segmentations. 16 files changed, 40 insertions(+) create mode 100644 derivatives/labels/sub-P002/anat/sub-P002_UNIT1_seg-manual.json create mode 100644 derivatives/labels/sub-P002/anat/sub-P002_UNIT1_seg-manual.nii.gz create mode 100644 derivatives/labels/sub-P005/anat/sub-P005_UNIT1_seg-manual.json create mode 100644 derivatives/labels/sub-P005/anat/sub-P005_UNIT1_seg-manual.nii.gz create mode 100644 derivatives/labels/sub-P007/anat/sub-P007_UNIT1_seg-manual.json create mode 100644 derivatives/labels/sub-P007/anat/sub-P007_UNIT1_seg-manual.nii.gz create mode 100644 derivatives/labels/sub-P013/anat/sub-P013_UNIT1_seg-manual.json create mode 100644 derivatives/labels/sub-P013/anat/sub-P013_UNIT1_seg-manual.nii.gz create mode 100644 derivatives/labels/sub-P024/anat/sub-P024_UNIT1_seg-manual.json create mode 100644 derivatives/labels/sub-P024/anat/sub-P024_UNIT1_seg-manual.nii.gz create mode 100644 derivatives/labels/sub-P033/anat/sub-P033_UNIT1_seg-manual.json create mode 100644 derivatives/labels/sub-P033/anat/sub-P033_UNIT1_seg-manual.nii.gz create mode 100644 derivatives/labels/sub-P034/anat/sub-P034_UNIT1_seg-manual.json create mode 100644 derivatives/labels/sub-P034/anat/sub-P034_UNIT1_seg-manual.nii.gz create mode 100644 derivatives/labels/sub-P035/anat/sub-P035_UNIT1_seg-manual.json create mode 100644 derivatives/labels/sub-P035/anat/sub-P035_UNIT1_seg-manual.nii.gz julien-macbook:~/data.neuro/basel-mp2rage $ git annex copy --to=origin copy derivatives/labels/sub-P001/anat/sub-P001_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P002/anat/sub-P002_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P002/anat/sub-P002_UNIT1_seg-manual.nii.gz (to origin...) ok copy derivatives/labels/sub-P003/anat/sub-P003_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P004/anat/sub-P004_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P005/anat/sub-P005_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P005/anat/sub-P005_UNIT1_seg-manual.nii.gz (to origin...) ok copy derivatives/labels/sub-P006/anat/sub-P006_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P007/anat/sub-P007_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P007/anat/sub-P007_UNIT1_seg-manual.nii.gz (to origin...) ok copy derivatives/labels/sub-P010/anat/sub-P010_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P011/anat/sub-P011_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P012/anat/sub-P012_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P013/anat/sub-P013_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P013/anat/sub-P013_UNIT1_seg-manual.nii.gz (to origin...) ok copy derivatives/labels/sub-P014/anat/sub-P014_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P015/anat/sub-P015_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P016/anat/sub-P016_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P017/anat/sub-P017_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P019/anat/sub-P019_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P021/anat/sub-P021_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P022/anat/sub-P022_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P023/anat/sub-P023_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P024/anat/sub-P024_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P024/anat/sub-P024_UNIT1_seg-manual.nii.gz (to origin...) ok copy derivatives/labels/sub-P025/anat/sub-P025_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P026/anat/sub-P026_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P027/anat/sub-P027_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P028/anat/sub-P028_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P029/anat/sub-P029_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P030/anat/sub-P030_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P031/anat/sub-P031_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P033/anat/sub-P033_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P033/anat/sub-P033_UNIT1_seg-manual.nii.gz (to origin...) ok copy derivatives/labels/sub-P034/anat/sub-P034_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P034/anat/sub-P034_UNIT1_seg-manual.nii.gz (to origin...) ok copy derivatives/labels/sub-P035/anat/sub-P035_UNIT1_lesion-manual.nii.gz ok copy derivatives/labels/sub-P035/anat/sub-P035_UNIT1_seg-manual.nii.gz (to origin...) ok copy sub-P001/anat/sub-P001_UNIT1.nii.gz ok copy sub-P002/anat/sub-P002_UNIT1.nii.gz ok copy sub-P003/anat/sub-P003_UNIT1.nii.gz ok copy sub-P004/anat/sub-P004_UNIT1.nii.gz ok copy sub-P005/anat/sub-P005_UNIT1.nii.gz ok copy sub-P006/anat/sub-P006_UNIT1.nii.gz ok copy sub-P007/anat/sub-P007_UNIT1.nii.gz ok copy sub-P010/anat/sub-P010_UNIT1.nii.gz ok copy sub-P011/anat/sub-P011_UNIT1.nii.gz ok copy sub-P012/anat/sub-P012_UNIT1.nii.gz ok copy sub-P013/anat/sub-P013_UNIT1.nii.gz ok copy sub-P014/anat/sub-P014_UNIT1.nii.gz ok copy sub-P015/anat/sub-P015_UNIT1.nii.gz ok copy sub-P016/anat/sub-P016_UNIT1.nii.gz ok copy sub-P017/anat/sub-P017_UNIT1.nii.gz ok copy sub-P019/anat/sub-P019_UNIT1.nii.gz ok copy sub-P021/anat/sub-P021_UNIT1.nii.gz ok copy sub-P022/anat/sub-P022_UNIT1.nii.gz ok copy sub-P023/anat/sub-P023_UNIT1.nii.gz ok copy sub-P024/anat/sub-P024_UNIT1.nii.gz ok copy sub-P025/anat/sub-P025_UNIT1.nii.gz ok copy sub-P026/anat/sub-P026_UNIT1.nii.gz ok copy sub-P027/anat/sub-P027_UNIT1.nii.gz ok copy sub-P028/anat/sub-P028_UNIT1.nii.gz ok copy sub-P029/anat/sub-P029_UNIT1.nii.gz ok copy sub-P030/anat/sub-P030_UNIT1.nii.gz ok copy sub-P031/anat/sub-P031_UNIT1.nii.gz ok copy sub-P033/anat/sub-P033_UNIT1.nii.gz ok copy sub-P034/anat/sub-P034_UNIT1.nii.gz ok copy sub-P035/anat/sub-P035_UNIT1.nii.gz ok (recording state in git...) julien-macbook:~/data.neuro/basel-mp2rage $ git push fatal: The current branch jca/corrected-segs has no upstream branch. To push the current branch and set the remote as upstream, use git push --set-upstream origin jca/corrected-segs julien-macbook:~/data.neuro/basel-mp2rage $ ```
jcohenadad commented 2 years ago

When trying the git suggestion, it does seem to do the job:

julien-macbook:~/data.neuro/basel-mp2rage $ git push --set-upstream origin jca/corrected-segs
Enumerating objects: 55, done.
Counting objects: 100% (55/55), done.
Delta compression using up to 16 threads
Compressing objects: 100% (27/27), done.
Writing objects: 100% (36/36), 3.61 KiB | 1.81 MiB/s, done.
Total 36 (delta 9), reused 0 (delta 0)
To data.neuro.polymtl.ca:datasets/basel-mp2rage
 * [new branch]      jca/corrected-segs -> jca/corrected-segs
Branch 'jca/corrected-segs' set up to track remote branch 'jca/corrected-segs' from 'origin'.
julien-macbook:~/data.neuro/basel-mp2rage $

So we should probably update the documentation for:

Changing:

git push

for:

git push --set-upstream origin <BRANCH>