Data

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/
└── 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

Note

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

Note

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