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
    └── anat
        └── sub-siteX01_T1w_reg.nii.gz
        └── sub-siteX01_T1w_reg.json
        └── sub-siteX01_T2w_reg.nii.gz
        └── sub-siteX01_T2w_reg.json
        └── sub-siteX01_acq-MTon_MTS_reg.nii.gz
        └── sub-siteX01_acq-MTon_MTS_reg.json
        └── sub-siteX01_acq-MToff_MTS_reg.nii.gz
        └── sub-siteX01_acq-MToff_MTS_reg.json
        └── sub-siteX01_acq-T1w_MTS.nii.gz
        └── sub-siteX01_acq-T1w_MTS.json
        └── sub-siteX01_T2star_reg.nii.gz
        └── sub-siteX01_T2star_reg.json
└── derivatives
    └── labels
        └── sub-siteX01
            └── anat
                └── sub-siteX01_T1w_seg.nii.gz

Note

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