Automatic segmentation of epilepsy neurosurgery resection cavity.
Project description
RESSEG
Automatic segmentation of postoperative brain resection cavities.
Installation
It's recommended to use conda and install your desired PyTorch version before
installing resseg.
A 6-GB GPU is large enough to segment an image in the MNI space.
conda create -n resseg python=3.8 ipython -y && conda activate resseg # recommended
pip install resseg
Usage examples
BITE
Example using an image from the Brain Images of Tumors for Evaluation database (BITE).
BITE=`resseg-download bite`
resseg $BITE -o bite_seg.nii.gz
tiohd --plot bite_seg.nii.gz
EPISURG
Example using an image from the EPISURG dataset.
Segmentation works best when images are in the MNI space, so resseg includes a tool
for this purpose (requires ANTsPy).
EPISURG=`resseg-download episurg`
resseg-mni $EPISURG -t episurg_to_mni.tfm
resseg $EPISURG -o episurg_seg.nii.gz -t episurg_to_mni.tfm
tiohd --plot episurg_seg.nii.gz
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