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How can I segment MRI to generate a 3D model?

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Friedman MAHARILAZA
Friedman MAHARILAZA on 4 Feb 2018
Edited: Petorr on 20 Feb 2018
How can I segment MRI to generate a 3D model?

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Walter Roberson
Walter Roberson on 4 Feb 2018
There is no built in "segmentMRI3" function, so that is an algorithm question that you should be researching in scientific papers and textbooks.

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Petorr
Petorr on 20 Feb 2018
Edited: Petorr on 20 Feb 2018
SPM12 is a free matlab package that performs automatic extraction of gray matter, white matter, csf, skull, and scalp from T1 weighted MRI. SPM outputs probability-weighted tissue mask images, with the same dimensions as the input. This would be a good starting point to make/edit 3D models.
Papers: Ashburner J, Friston KJ. Unified segmentation. Neuroimage. 2005 Ashburner J. SPM: a history. Neuroimage. 2012
There are also various other automatic brain MRI segmentation tools, mostly running in Linux. E.g., FreeSurfer is a very powerful one that outputs brain surface maps as 3D vertex mesh data.

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