Slicer Brats Preprocessor is the wrapper for performing the preprocessing steps of the brattoolkit. The brats-toolkit will be installed automatically with the first use of the module.
For installing the docker installation follow the steps on https://github.com/UWA-Medical-Physics/SlicerBatchBrainMRTumorSegmentation.
Slicer scriptedcli module for brats preprocessor steps. Following the GUI for the brats preprocessor.
The inputs are:
- Directory path to the patients data
- Flair file path
- T1 file path
- T2 file path
- T1c file path
The outputs from the brats preprocessor are the following folders.
The outputs from the first folder are used to perform further processing in the pipeline. The segmentation of the pre-processed data. For segmenting the above acquired preprocessed data, use the SlicerBratsSegmentator module. https://github.com/UWA-Medical-Physics/SlicerBratsSegmentator