Measuring thickness

how can I measure thickness in every point of the object and report with a color map
image
like this photo?

If you have two models, one of the inner surface and one of the outer surface you could use this extension:

https://www.slicer.org/wiki/Documentation/4.8/Extensions/ModelToModelDistance

Or if you means specifically you want to measure cortical thickness from mri you could look into Freesurfer (http://surfer.nmr.mgh.harvard.edu/)

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I want to perform cortical thickness analysis on a closed surface, isn’t this possible in the slicer at all?

Can you be more specific about what you need and why freesurfer doesn’t already do it? Slicer does a lot of things but we try not to duplicate tools that already exist.

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I need to do thickness analyzing in slicer, freesurfer is only on mac and linux which I don’t have and also is huge(4.4-4.6GB) so I would rather to do this with slicer

Sorry, I don’t think there’s any easy way to do that.

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Options:

  • run in a virtual machine (VirtualBox is free; I think VMWare Player or current equivalent is also still free and has better graphics performance)
  • if you have up-to-date Windows 10, you may be able to run under Windows Subsystem for Linux; someone posted instructions here:

http://nuclear-imaging.info/site_content/2016/09/12/installing-running-freesurfer-windows-10/

(the second option will probably be faster and use less memory, but will have somewhat lower i/o performance and possibly unknown bugs if you hit unsupported syscalls)

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tnx can you help me how I can do this after the installation?

Please follow the FreeSurfer support instructions and contact them with further questions.

https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSupport