Push rootlets segmentations

[valosekj]

Currently, the manual rootlets GT segmentations (n=36; see D5.tsv) used to train the latest model M5 are stored locally on duke (~/duke/projects/ml_spinal_rootlets/datasets/Dataset012_M5) organized according to the nnUNet format:

├── imagesTr
│   ├── sub-002_ses-headNormal_000_0000.nii.gz
│   ├── sub-003_ses-headNormal_002_0000.nii.gz
...
├── imagesTs
│   ├── sub-007_ses-headNormal_009_0000.nii.gz
│   ├── sub-010_ses-headUp_015_0000.nii.gz
│   ├── sub-amu02_215_0000.nii.gz
│   ├── sub-barcelona01_212_0000.nii.gz
│   └── sub-brnoUhb03_209_0000.nii.gz
├── labelsTr
│   ├── sub-002_ses-headNormal_000.nii.gz
│   ├── sub-003_ses-headNormal_002.nii.gz
...
└── labelsTs
    ├── sub-007_ses-headNormal_009.nii.gz
    ├── sub-010_ses-headUp_015.nii.gz
    ├── sub-amu02_215.nii.gz
    ├── sub-barcelona01_212.nii.gz
    └── sub-brnoUhb03_209.nii.gz

TODO

• convert the GT used for training (labelsTr) from nnUNet format to BIDS using convert_nnUNetV2_to_bids.py
• choose the proper suffix -- according to our intranet, it should be sub-001_acq-sag_T2w_label-rootlets_dseg.nii.gz
• push the GT to spine-generic multi-subject - done in Add T2w dorsal rootlets labels spine-generic/data-multi-subject#158
• push the GT to openneuro/ds004507 - done in https://openneuro.org/datasets/ds004507/versions/1.1.0

Note that for five testing images (imagesTs) we have available reference STAPLE segmentations (labelsTs) and also manual segmentations from 4 raters. These segs are already BIDSified (/duke/projects/ml_spinal_rootlets/datasets/inter-rater_variability):

details

derivatives/labels
├── sub-007
│   └── ses-headNormal
│       └── anat
│           ├── sub-007_ses-headNormal_T2w_label-rootlet_rater1.nii.gz
│           ├── sub-007_ses-headNormal_T2w_label-rootlet_rater2.nii.gz
│           ├── sub-007_ses-headNormal_T2w_label-rootlet_rater3.nii.gz
│           ├── sub-007_ses-headNormal_T2w_label-rootlet_rater4.nii.gz
│           └── sub-007_ses-headNormal_T2w_label-rootlet_staple.nii.gz
├── sub-010
│   └── ses-headUp
│       └── anat
│           ├── sub-010_ses-headUp_T2w_label-rootlet_rater1.nii.gz
│           ├── sub-010_ses-headUp_T2w_label-rootlet_rater2.nii.gz
│           ├── sub-010_ses-headUp_T2w_label-rootlet_rater3.nii.gz
│           ├── sub-010_ses-headUp_T2w_label-rootlet_rater4.nii.gz
│           └── sub-010_ses-headUp_T2w_label-rootlet_staple.nii.gz
├── sub-amu02
│   └── anat
│       ├── sub-amu02_T2w_label-rootlet_rater1.nii.gz
│       ├── sub-amu02_T2w_label-rootlet_rater2.nii.gz
│       ├── sub-amu02_T2w_label-rootlet_rater3.nii.gz
│       ├── sub-amu02_T2w_label-rootlet_rater4.nii.gz
│       └── sub-amu02_T2w_label-rootlet_staple.nii.gz
├── sub-barcelona01
│   └── anat
│       ├── sub-barcelona01_T2w_label-rootlet_rater1.nii.gz
│       ├── sub-barcelona01_T2w_label-rootlet_rater2.nii.gz
│       ├── sub-barcelona01_T2w_label-rootlet_rater3.nii.gz
│       ├── sub-barcelona01_T2w_label-rootlet_rater4.nii.gz
│       └── sub-barcelona01_T2w_label-rootlet_staple.nii.gz
└── sub-brnoUhb03
    └── anat
        ├── sub-brnoUhb03_T2w_label-rootlet_rater1.nii.gz
        ├── sub-brnoUhb03_T2w_label-rootlet_rater2.nii.gz
        ├── sub-brnoUhb03_T2w_label-rootlet_rater3.nii.gz
        ├── sub-brnoUhb03_T2w_label-rootlet_rater4.nii.gz
        └── sub-brnoUhb03_T2w_label-rootlet_staple.nii.gz

[jcohenadad]

choose the proper suffix -- according to our intranet, it should be sub-001_acq-sag_T2w_label-rootlets_dseg.nii.gz

we also need to find a way to distinguish rater1, rater2, staple, etc. Maybe @NathanMolinier has some ideas

[NathanMolinier]

we also need to find a way to distinguish rater1, rater2, staple, etc. Maybe @NathanMolinier has some ideas

To differentiate between raters and staple, I think that we could use the entity desc-XXX (desc-rater1, desc-staple etc.). See BIDS specification.

Also, if we want to clarify the meaning of these desc entities, we could also add a file descriptions.tsv at the root of the derivative folder as shown on our intranet here.

[valosekj]

Completed within:

• Add T2w dorsal rootlets labels spine-generic/data-multi-subject#158
• https://openneuro.org/datasets/ds004507/versions/1.1.0