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MUSHAR:

A MATLAB toolbox for three-dimensional reconstruction and analysis of MUscle SHape and ARchitecture.

MUSHAR-toolbox

Features

  1. Establish point-to-point correspondence on surfaces and inside volumes through non-rigid registration of distance maps.
  2. Reconstruction of group-averaged muscle shape and muscle fibre orientations from magnetic resonance imaging and diffusion tensor imaging data.
    1. Includes code for averaging and interpolating diffusion tensors in the log-Euclidean domain
  3. Statistical analysis of local changes in shape and fibre orientations.
  4. Visualization of changes in shape and fibre orientations.

Installation

  • Install Matlab (developed and tested in version R2019b)
  • Add the MUSHAR-toolbox to the Matlab path.

The following software tools should be installed and made available on the command line:

  • Shapeworks (tested in version 6.2.1 - older versions may not be compatible)
  • Elastix (developed and tested in version 4.7)
  • Convert3D

Getting started

  • Run the demo scripts to guide you through the main steps.
  • Modify the scripts to set up your own analysis.

Citation

Please cite the following paper when using this toolbox:

Bolsterlee, B., 2022. A new framework for analysis of three-dimensional shape and architecture of human skeletal muscles from in vivo imaging data. Journal of Applied Physiology 132, p712-725. link

(Or read the preprint here.)