Generate head surface

mohammadrezarezaeid · February 26, 2023, 7:44am

Hello,

I am trying to understand Generate head surface function, but some questions come to my mind that I want to ask. First of all, How does Brainstorm define the head surface? Is this only a global thresholding segmentation or do you apply other functions too?
Secondly, How does Brainstorm define the curvature after applying the Generate head surface function? which algorithm does it use?
Finally, I will be very happy if anybody put the git link of the Generate head surface function here.

Thank you so much

Francois · February 27, 2023, 10:59am

I am trying to understand Generate head surface function, but some questions come to my mind that I want to ask. First of all, How does Brainstorm define the head surface? Is this only a global thresholding segmentation or do you apply other functions too?

The options for computing the head surface are documented here:
https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer#The_head_surface_looks_bad

The commented code is available in the function tess_isohead.m:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/anatomy/tess_isohead.m

function [HeadFile, iSurface] = tess_isohead(iSubject, nVertices, erodeFactor, fillFactor, Comment)
% TESS_GENERATE: Reconstruct a head surface based on the MRI, based on an isosurface
%
% USAGE:  [HeadFile, iSurface] = tess_isohead(iSubject, nVertices=10000, erodeFactor=0, fillFactor=2, Comment)
%         [HeadFile, iSurface] = tess_isohead(MriFile,  nVertices=10000, erodeFactor=0, fillFactor=2, Comment)
%         [Vertices, Faces]    = tess_isohead(sMri,     nVertices=10000, erodeFactor=0, fillFactor=2)
%
% If input is loaded MRI structure, no surface file is created and the surface vertices and faces are returned instead.

% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
% 
% Copyright (c) University of Southern California & McGill University
% This software is distributed under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPLv3
% license can be found at http://www.gnu.org/copyleft/gpl.html.
% 
% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
% UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY

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Secondly, How does Brainstorm define the curvature after applying the Generate head surface function? which algorithm does it use?

The curvature of a surface is computed by tess_curvature.m, but this is not very meaningful for the head surface. It is mostly used for displaying as darker areas the bottom of the cortical sulci: