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You can print from the surfaces. Using

mris_convert --combinesurfs $SUBJECTS_DIR/${subject}/surf/lh.pial $SUBJECTS_DIR/${subject}/surf/rh.pial \ $SUBJECTS_DIR/cortical.stl

will take the pial surfaces from both hemispheres and combine them into a single STL file compatible with many printers. To go from a volumetric file like aparc or aseg, you'd need to binarize your volume and use mri_tessellate to make a surface mesh around it and mris_convert to make an STL from the mesh, but that's just extra steps when you have the surface outputs from FS already.

Either way, you may need to do some post-processing in a CAD program to make the resulting mesh more printer-friendly. If you want to include cerebellum and brainstem as well, you will need to 1) extract and binarize the ROIs, 2) use mri_tessellate to get surfaces and mris_convert to get STL format, and 3) merge the cortical STL with the cerebellar/brainstem STL.

Michael Notter has a nice set of scripts (using FSL for cerebellum and brainstem rather than FS) that walk you through putting together the final whole-brain STL file for printing: https://secure-web.cisco.com/1BvbhU8GaBWBicxBZZUAUX-wSoz7hnR2gLOFIO_YUkei8jz...

On Tue, Aug 15, 2023 at 8:24 AM Pukovisa Prawiroharjo pukovisa@ui.ac.id wrote:

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can we print the aseg and aparc image in fresurfer to 3D model for print it in 3D printer?

best regards

*Pukovisa Prawiroharjo, M.D., Sp.N, Subsp. NGD (K), PhD* Neurobehavior Consultant, Neurology Specialist Neurology Department, Faculty of Medicine, Universitas Indonesia Chair of Bioethics Cluster IMERI UI Chair of International Policy Div, Board of Development Med Services IDI

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