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Automatic segmentation of epilepsy neurosurgery resection cavity.

Project description


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.

`shell 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)](

`shell 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](

`shell 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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