Brain Extraction

[Niko-k98]

Is the Brain extraction and masking currently functional in this repo or should I stick to the BraTS tool-kit repo for the time being?

[neuronflow]

It is functional. However, the documentation and tutorials still need to be prepared.

What is the issue you are facing?

You can use the package like this:
https://github.com/BrainLesion/preprocessing/blob/main/example_modality_centric_preprocessor.py

For brain extraction, set bet to True for each modality you want to skullstrip.

[Niko-k98]

I just wanted to verify functionality. i was able to get it to work on an nrrd file of an mri, however the deskulled output had less slices than the initial file, is this to be expected? Thank you for your assistance

[neuronflow]

so far I tested the pipeline with .nii.gz files. No experience with nrrd yet.

You can use any file structure you want. You just need to provide input and output paths.

Output files will have the resolution of the SRI24 atlas:
155x240x240

[neuronflow]

closed until more information is provided.

[neuronflow]

@Niko-k98
we now have some API changes and a first small tutorial:
https://github.com/BrainLesion/tutorials/tree/main/preprocessing

Your feedback is appreciated :)