LesionMap

LesionMap is a comprehensive package for normalization and visualization of volumetric imaging segments. Users can perform segmentation, normalization, and visualization of large datasets with very few lines of code.

Install

pip install LesionMap

Usage

1) Segment your scans

config.py preprocess.py preprocess_2d_images.py predict.py

scripts are part of the DeepSeg toolkit to automatically segment scans. If you are manually segmenting scans (with 3D slicer for example), you can skip these steps.

2) Normalize scans to Montreal Neurological Institute brain space

python3 warp.py normalizes segments to common MNI brain space. MNI template can be downloaded here: https://neuroconductor.org/help/MNITemplate/

3) Make your heatmap

python3 heatmap.py makes a 3D matrix of masks and maps them onto a common average brain