Corresponding author: Christopher R Madan (
Academic editor:
Brain morphology can provide insights into inter-individual differences. In the present guide, we outline the steps for generating a print-ready 3D model of brain structures from a standard T1-weighted structural MRI volume. By improving our understanding of brain morphology, we hope to enhance teaching and scientific communication, as well as aid in the development of novel measures of brain morphology.
The present guide details the steps for generating a print-ready 3D model of brain structures from a standard T1-weighted structural MRI volume.
CRM is supported by a fellowship from the Canadian Institutes of Health Research (FRN-146793).
Recent research has demonstrated that shape-related properties (i.e., morphology) of the brain can be useful in characterizing inter-individual differences (e.g.,
The processing pipeline used to produce a print-ready mesh is outlined in Fig.
After the FreeSurfer pipeline has been run, the remaining steps can be executed within a few minutes, provided the necessary programs are already installed. Nearly all of these remaining steps can be executed via a command-line interface, with the commands listed in Table
First, the cortical surface files (
For 3D printing, meshes usually need to be 'repaired' to ensure that there are no holes or other issues with the mesh structure (cf.
(Also see
The resulting files (.
The code for converting and decimating the meshes was modified from Roberto Toro's
CRM is supported by a fellowship from the Canadian Institutes of Health Research (FRN-146793).
To compile tridecimator, you need to run two commands (from inside the vcglib/apps/tridecimator directory):
[1] qmake tridecimator.pro
This should generate a few files, including 'Makefile'.
[2] make
You should now have 'tridecimator' (no file extension) – this is the actual executable program. (I get 1 warning when I compile, but this is fine.)
If you don't have qmake installed, see
Illustration of the processing pipeline involved in converting a structural MRI volume to a print-ready surface mesh.
Photos of a resulting 3D-printed surface. (A) View of the full models. (B) Close-up of the coronal cross-section. (C) Close-up of the lateral surface. (D) Photo of the Machina Mk2 X20 printers used to print the models, located at the University of Alberta Libraries.
Code
1 |
mg=/Applications/Research/imaging/meshgeometry/meshgeometry_mac |
Surface meshes (.ply) from FreeSurfer subject 'bert'.
Data type: surface mesh
File: oo_99702.zip