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Automatic segmentation of epilepsy neurosurgery resection cavity.

Project description


Automatic segmentation of postoperative brain resection cavities.


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


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


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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