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MR-TIM: MR-based head tissue modelling is open source MATLAB software for head tissue modelling from structural magnetic resonance (MR) images.

It performs automated segmentation of whole-head T1-weighted MR images in 12 tissues:

  • brain gray matter (GM)
  • cerebellar GM
  • brain white matter (WM)
  • cerebellar WM
  • brainstem
  • cerebrospinal fluid (CSF)
  • spongy bone
  • compact bone
  • muscle
  • fat
  • eyes
  • skin


MR-TIM requires MATLAB 2016b (MathWorks) or later versions and it is intended as a toolbox for SPM12 software package.

To install and use the software, read the user guide.


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