repositories

Each model is saved in its own repository under the ivadomed organization. The convention for naming repositories is the following:

model_task_animal_pathology_region_contrast_architecture

Should be small letters only.

Fields:
- task = {seg, label, find}, default=seg
- animal = {human, dog, cat, rat, mouse, ...}, default=human
- pathology = {ms, sci}
- region = {sc, gm, csf, brainstem, axon, myelin, ...}, default=sc
- contrast = {t1, t2, t2star, dwi, sem, tem, oi, ...}, default=None
- architecture = {unet2d, unet3d, filmCharley, hemisAndreanne}, default=unet2d

Examples: 

model_seg_monkey_sc_t1_unet3d

# multi-channel, multi-class
model_seg_sc-gm_t1-t2_unet3d

Packaging models

Models to be used by 3rd party software (e.g. SCT) should be uploaded as 'assets' to a release of the repository. The steps are:

• Create a release of the repository. The tag and title of the release should be rYYYYMMDD, example: r20211223.
• Put the model and JSON file inside a folder that has the name of the model.
• Zip the folder and upload it as an asset in the release
• Publish the release.

Data

Convention:
data_purpose_study_animal_anatomy_contrast

Fields:
- purpose = {testing, example, tumor, ms, ...}
- study = {}  Study associated with the dataset
- animal = {human, dog, cat, rat, mouse, ...}, default=human
- anatomy = {sc, brainstem, brain, foot, ...}, default=sc
- contrast = {t1, t2, t2star, dwi, sem, tem, oi, ...}, default=None

Examples:
- data_testing
- data_example_spinegeneric
- data_axondeepseg_sem

Derivatives

⚠️ Be aware of the updated convention available on intranet.

This is a folder at the root of the dataset, which includes derivatives from the data, including manual segmentations/labeling to use as ground truth for training. According to BIDS, these data should go under derivatives/ folder, and follow the same folder logic as the sub-* data. Example:

    data-multi-subject
    │
    ├── dataset_description.json
    ├── participants.json
    ├── participants.tsv
    ├── sub-ubc01
    ├── sub-ubc02
    ├── sub-ubc03
    ├── sub-ubc04
    ├── sub-ubc05
    ├── sub-ubc06
    │   │
    │   ├── anat
    │   │   ├── sub-ubc06_T1w.json
    │   │   ├── sub-ubc06_T1w.nii.gz
    │   │   ├── sub-ubc06_T2star.json
    │   │   ├── sub-ubc06_T2star.nii.gz
    │   │   ├── sub-ubc06_T2w.json
    │   │   ├── sub-ubc06_T2w.nii.gz
    │   │   ├── sub-ubc06_acq-MToff_MTS.json
    │   │   ├── sub-ubc06_acq-MToff_MTS.nii.gz
    │   │   ├── sub-ubc06_acq-MTon_MTS.json
    │   │   ├── sub-ubc06_acq-MTon_MTS.nii.gz
    │   │   ├── sub-ubc06_acq-T1w_MTS.json
    │   │   └── sub-ubc06_acq-T1w_MTS.nii.gz
    │   │
    │   └── dwi
    │       ├── sub-ubc06_dwi.bval
    │       ├── sub-ubc06_dwi.bvec
    │       ├── sub-ubc06_dwi.json
    │       ├── sub-ubc06_dwi.nii.gz
    │       ├── (sub-ubc06_acq-b0_dwi.json)
    │       └── (sub-ubc06_acq-b0_dwi.nii.gz)
    │
    └── derivatives
        │
        └── labels
            └── sub-ubc06
                │
                ├── anat
                │   ├── sub-ubc06_T1w_seg-manual.nii.gz  <---------- manually-corrected spinal cord segmentation.
                │   ├── sub-ubc06_T1w_seg-manual.json  <------------ information about origin of segmentation (see below). Note: this file is optional for ivadomed's loader.
                │   ├── sub-ubc06_T1w_labels-disc-manual.nii.gz  <------- intervertebral disc labels. Voxel located at the posterior tip of each disc. The value corresponds to the disc, e.g.: C2/C3: value=3, C3/C4: value=4, etc.
                │   ├── sub-ubc06_T1w_labels-disc-manual.json
                │   ├── sub-ubc06_T2star_gmseg-manual.nii.gz  <------- manually-corrected gray matter segmentation
                │   ├── sub-ubc06_T2star_gmseg-manual.json
                │   ├── sub-ubc06_T2star_lesion-manual.nii.gz  <------- lesion segmentation
                │   └── sub-ubc06_T2star_lesion-manual.json
                │
                └── dwi
                    ├── sub-ubc06_dwi_moco_dwi_mean_seg-manual.nii.gz  <-- manually-corrected spinal cord segmentation
                    └── sub-ubc06_dwi_moco_dwi_mean_seg-manual.json

The convention for suffix is the following:

_task-region

Fields:
- task = {seg, label}, default=seg
- region = {sc, gm, csf, brainstem, tumor, edema, cavity, lesion, disc, axon, myelin}, default=sc

The .json file includes the following information:

{
    "Author": "Bob Dylan",
    "Date": "2020-07-29 21:25:37"
}