https://www.artefact.tk/software/matlab/gifti/
This MATLAB class allows to handle GIfTI Geometry file format from the Neuroimaging Informatics Technology Initiative.
It relies on external libraries:
- Base64, by Peter J. Acklam: http://home.online.no/~pjacklam/
- miniz, by Rich Geldreich: https://github.com/richgel999/miniz
- dzip, by Michael Kleder: https://www.mathworks.com/matlabcentral/fileexchange/8899
- XMLTree, by Guillaume Flandin: https://www.artefact.tk/software/matlab/xml/
- mVTK, by Guillaume Flandin: https://www.artefact.tk/software/matlab/mvtk/
- JSONio, by Guillaume Flandin: https://www.artefact.tk/software/matlab/jsonio/
Note that these tools are already included in the GIfTI library provided here, so you don't need to install them separately.
This library is also part of SPM:
MATLAB 7.1 (R14SP3) or above is required to use most of the features of this toolbox.
This library takes advantage of MATLAB Object-Oriented facilities and all
the code is embedded in a @gifti
class. To install it, all you need is to
make sure that the directory containing @gifti
is in MATLAB path:
addpath /home/login/Documents/MATLAB/gifti
The handling of gzipped data requires a C-MEX file to be compiled, see
@gifti/private/zstream.c
. A Java alternative will be used otherwise,
in which case MATLAB should not be started with the '-nojvm'
option
In the following, we use the files contained in BV_GIFTI.tar.gz
(BrainVISA examples), available from the NITRC website:
http://www.nitrc.org/frs/?group_id=75&release_id=123
% Read the GIfTI surface file
g = gifti('sujet01_Lwhite.surf.gii')
% Read the GIfTI shape file
gg = gifti('sujet01_Lwhite.shape.gii')
% Display mesh
figure; plot(g);
% Display mesh with curvature
figure; plot(g,gg);
In a similar way, a gifti object can be created from scratch and save to a file:
load mri
D = squeeze(D);
Ds = smooth3(D);
g = gifti(isosurface(Ds,5))
h = plot(g);
daspect([1,1,.4]); view(45,30); axis tight
lightangle(45,30);
set(h,'SpecularColorReflectance',0,'SpecularExponent',50)
save(g,'mri.surf.gii','Base64Binary');
MATLAB is a Registered Trademark of The Mathworks, Inc.
Copyright (C) 2008-2019 Guillaume Flandin Guillaume@artefact.tk