Data

Without data, nothing can be done. To get you started, we recommend you download the Spinal Cord MRI Public Database. This dataset is composed of 248+ subjects from different imaging centers and includes original images in NIfTI format as well as manual segmentations and labels. The data are organized according to the BIDS convention, to be fully compatible with ivadomed loader:

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.

Warning

TODO: Update openneuro site to include derivatives