resseg 0.3.2

# 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.

`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)](http://nist.mni.mcgill.ca/?page_id=672).

`shell 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](https://doi.org/10.5522/04/9996158.v1). Segmentation works best when images are in the MNI space, so resseg includes a tool for this purpose (requires [ANTsPy](https://antspyx.readthedocs.io/en/latest/?badge=latest)).

`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 `