The latest dataset can be downloaded from the Harvard Dataverse repository.
The patients are grouped into several tumor categories based on their origins. Each patient for any tumor category has the same naming format, such as
001-Glioma-AYEY
| flair.nii.gz
| t1.nii.gz
| t2.nii.gz
| t1ce.nii.gz
| flair_seg_label1.nii.gz
| t1ce_seg_label2.nii.gz
In this case, 001-Glioma-AYEY is the general patient ID, 001 is the patient number, Glioma is the tumor category, AYEY is the center ID, flair_seg_label1 is the segmentation mask of Label 1 derived from the FLAIR sequence, and t1ce_seg_label2 is the segmentation mask of Label 2 derived from the T1-ce sequence.
We provide a Docker container to segment MR images on your side. segment_one_subject.sh is the shell script to run the container on one subject. Please make sure:
(a) The FLAIR, T1, T1-ce, and T2 images have the same naming format as the 001-Glioma-AYEY example before.
(b) The nvidia-container-toolkit package is installed corrected.
We provide the shell pre-processing scripts based on existing packages. Please check the 'preprocessing' folder.