To facilitate the organization of data, ivadomed requires the data to be organized according to the Brain Imaging Data Structure (BIDS) convention. An example of this organization is shown below:

└── dataset_description.json
└── participants.tsv
└── sub-01  <--------------------- Folder enclosing data for subject 1
└── sub-02
└── sub-03
    └── anat
        └── sub-03_T1w.nii.gz  <-- MRI image in NIfTI format
        └── sub-03_T1w.json  <---- Metadata including image parameters, MRI vendor, etc.
        └── sub-03_T2w.nii.gz
        └── sub-03_T2w.json
└── derivatives
    └── labels
        └── sub-03
            └── anat
                └── sub-03_seg-tumor-manual.nii.gz  <-- Manually-corrected segmentation
                └── sub-03_seg-tumor-manual.json  <---- Metadata including author who performed the labeling and date


participants.tsv should, at least, include a column participant_id, which is used when loading the dataset.


For an exhaustive list of derivatives used in ivadomed, please see our wiki