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

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

[Walter Roberson]

There is no built in "segmentMRI3" function, so that is an algorithm question that you should be researching in scientific papers and textbooks.

Answer 1

[Petorr]

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.