Getting Started - GerardMJuan/BrainFortLib-neuroimage-hub GitHub Wiki

Neuroimages usually require of specific libraries and programs in order to interpret and work with them. Luckily, there are a wide range of software available for neuroimage processing and visualizing. Here I will put some links on this software.

Most of these tools are available in a wide range of operating systems, but some of them are only available on Linux.

Visualization tools

These are tools for visualizing image volumes. They are usually used on personal preference.+

  • MITK Workbench - Link One of the most used tools, ideal for visualization of volumes, masks and with a wide array of other helpful options.
  • BrainSuite - Link This one also integrates several preprocessing tools in an interactive way (non-command line). Can be useful for some experiments. I have only used it for visualization, though.
  • ITKSnap - Link Another open-source, free program to visualize 3D volumes of different modalities.

It the end, it all boils down to personal preference. Choose the program that suits you better.

Processing tools

  • ANTS - Link Very complete library, regarded as state of the art, for brain image processing and registration. Most of the scripts we will use use ANTS. Highly recommended to skim through the tools.
  • FSL - Link Widespread toolbox for analysis and processing of different modalities of brain images. It is really easy to use and install, and comes with both visual interface and command line scripts. Skull stripping and segmentation algorithms tools are very used.
  • Freesurfer - Link Freesurfer is a very extensive and big toolbox, also very used and with a lot of available documentation.
  • SPM - Link MATLAB library for image analysis. Also has a visual interface.

Most of the work and the pipelines already implemented and that we will use are based on the ANTS and FSL library.

Other useful links:

  • ADNI Database - Link We will use data from the ADNI database. In their web page they have a complete explanation of the different types of data available, the different acquisition methods and other useful information.
  • Useful compilation of open source programs and resources for medical imaging visualization: Link
  • Lectures on neuroimaging methods (I have not done them, but they seem cool enough): Link
  • For ANTS, the ANTS wiki has a section of examples and Frequently Asked Questions that is really informative: https://github.com/ANTsX/ANTs/wiki.

I think that it would be interesting to skim through the very complete documentation and examples of the various tools to familiarize with them.