Welcome to HyperMapp3r’s documentation!

HyperMapp3r (pronounced hypermapper) is a CNN-based segmentation algorithm of White Matter Hyperintensity(WMH) segmentation using MRI images from BrainLab. It can deal with brains with extensive atrophy and segments the wmh in seconds. It uses a T1-weighted, FLAIR, and brain mask images as the inputs and segments.

We recommend using HyperMapp3r with the Docker or Singularity containers we provide but it can also be installed locally. See our installation instructions for more information.

Copyright (C) 2020 AICONSLab.

Contents:

• Before installing HyperMapp3r
  • Acknowledging this work
  • Reference
  • License
• Local Install
  • Python
  • ANTs & Convert3D (c3d)
  • Installing package and dependencies for HippMapp3r locally
  • Download deep models
  • For tab completion
  • Updating HyperMapp3r
• Getting started
  • For GUI
  • For Command Line
  • WMH volumes
  • QC
  • Logs
  • File conversion
• Segmentation tutorials
  • GUI
  • Command Line
• Docker / Singularity
  • Before using Docker image for HyperMapp3r
  • Pulling HyperMapp3r’s Docker image
  • Running the Docker image
  • Using HyperMapper on Singularity