neuropoly / data-management

Repo that deals with datalad aspects for internal use
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`basel-mp2rage` - add manually corrected `lesion-manual3` segmentation #192

Closed valosekj closed 1 year ago

valosekj commented 1 year ago

Based on a discussion with @jcohenadad and @mchen1110, I added the lesion-manual3.nii.gz segmentation to the git-annex basel-mp2rage/derivatives. My branch is named jv/add_lesion-manual3_to_derivatives.

Specifically, I added the following 30 files: ``` $ cd basel-mp2rage/derivatives/labels $ ls -1 sub-P0*/anat/*manual3.nii.gz sub-P001/anat/sub-P001_UNIT1_lesion-manual3.nii.gz sub-P002/anat/sub-P002_UNIT1_lesion-manual3.nii.gz sub-P003/anat/sub-P003_UNIT1_lesion-manual3.nii.gz sub-P004/anat/sub-P004_UNIT1_lesion-manual3.nii.gz sub-P005/anat/sub-P005_UNIT1_lesion-manual3.nii.gz sub-P006/anat/sub-P006_UNIT1_lesion-manual3.nii.gz sub-P007/anat/sub-P007_UNIT1_lesion-manual3.nii.gz sub-P010/anat/sub-P010_UNIT1_lesion-manual3.nii.gz sub-P011/anat/sub-P011_UNIT1_lesion-manual3.nii.gz sub-P012/anat/sub-P012_UNIT1_lesion-manual3.nii.gz sub-P013/anat/sub-P013_UNIT1_lesion-manual3.nii.gz sub-P014/anat/sub-P014_UNIT1_lesion-manual3.nii.gz sub-P015/anat/sub-P015_UNIT1_lesion-manual3.nii.gz sub-P016/anat/sub-P016_UNIT1_lesion-manual3.nii.gz sub-P017/anat/sub-P017_UNIT1_lesion-manual3.nii.gz sub-P019/anat/sub-P019_UNIT1_lesion-manual3.nii.gz sub-P021/anat/sub-P021_UNIT1_lesion-manual3.nii.gz sub-P022/anat/sub-P022_UNIT1_lesion-manual3.nii.gz sub-P023/anat/sub-P023_UNIT1_lesion-manual3.nii.gz sub-P024/anat/sub-P024_UNIT1_lesion-manual3.nii.gz sub-P025/anat/sub-P025_UNIT1_lesion-manual3.nii.gz sub-P026/anat/sub-P026_UNIT1_lesion-manual3.nii.gz sub-P027/anat/sub-P027_UNIT1_lesion-manual3.nii.gz sub-P028/anat/sub-P028_UNIT1_lesion-manual3.nii.gz sub-P029/anat/sub-P029_UNIT1_lesion-manual3.nii.gz sub-P030/anat/sub-P030_UNIT1_lesion-manual3.nii.gz sub-P031/anat/sub-P031_UNIT1_lesion-manual3.nii.gz sub-P033/anat/sub-P033_UNIT1_lesion-manual3.nii.gz sub-P034/anat/sub-P034_UNIT1_lesion-manual3.nii.gz sub-P035/anat/sub-P035_UNIT1_lesion-manual3.nii.gz ```

TODO:

Related to https://github.com/ivadomed/model_seg_ms_mp2rage/issues/13

mguaypaq commented 1 year ago

Both git annex get and bids-validator . are happy with the changes. Merged into master!

valosekj commented 1 year ago

@mguaypaq Thank you!

jcohenadad commented 1 year ago

JSON file is missing-- pls add JSON file according to this doc and this doc:

ex:

{
  "Author": "Michelle Chen",
}
valosekj commented 1 year ago

JSON file is missing

Ahh, good catch! Thank you!

JSON files added in e54433f222965fb0b33fb62298d2cab7b7138711 commit to the jv/add_lesion-manual3_to_derivatives branch.

mguaypaq commented 1 year ago

Merged again.