Data

Organization

To facilitate the organization of data, ivadomed requires the data to be organized according to the Brain Imaging Data Structure (BIDS) standard. The details of the standard can be found in the BIDS specification.

Validation

The compliance of the dataset with BIDS can be validated with the BIDS-validator web version. Other options for validation are available here.

Examples

An example of this organization is shown below for MRI data:

dataset/
└── dataset_description.json
└── participants.tsv  <-------------------------------- Metadata describing subjects attributes e.g. sex, age, etc.
└── 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

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

For usage in ivadomed, additional examples are available in our tutorials, for MRI data and Microscopy data. Further examples of the BIDS organization can be found in the BIDS-examples repository.