In this repository the data files of OncoFEM are collected. These are in the following listed and cited where appropriate:

SRI24 atlas T1 and T2 MRI modalities (T. Rohlfing, N. M. Zahr, E. V. Sullivan, and A. Pfefferbaum, “The SRI24 multichannel atlas of normal adult human brain structure,” Human Brain Mapping, vol. 31, no. 5, pp. 798-819, 2010. doi: 10.1002/hbm.20906) Tutorial files: Because of long calculation times particular interim results are provided
generated geometry (geometry.xdmf + geometry.h5) edema mapping (edema.xdmf + edema.h5) cerebrospinal fluid distribution file (csf.nii.gz) white matter distribution (wm.nii.gz) grey matter distribution (gm.nii.gz) Segmented tumor distribution, class 0 (tumor_class_pve_0.nii.gz) Segmented tumor distribution, class 1 (tumor_class_pve_1.nii.gz) Segmented tumor distribution, class 2 (tumor_class_pve_2.nii.gz) Folder of magnetic resonance images of first Authors head in DICOM format (T1 and Flair modality) First six datasets (T1, T1ce, T2, Flair, tumour segmentation) of BraTS 2020 collection (https://www.med.upenn.edu/cbica/brats2020/data.html)

Five different weights of tumor segmentations with different input channels. Herein, either one of T1, T1ce, T2, Flair or all of them are used. Additionally, an empty image is included for an adaptive training.

The data corresponds to OncoFEM version 1.0.

The up-to-date Version of oncofem can be obtained from github or Version 1.0 from DaRUS, which comes in a pre-installed virtual box.

For usage, download and unzip file next to the oncofem folder or adjust the paths stored in the config.ini file if the files need to be somewhere else.