GIfTI - a MATLAB GIfTI Library (v1.6)

This MATLAB class allows to handle GIfTI Geometry file format from the Neuroimaging Informatics Technology Initiative.

GIfTI: http://www.nitrc.org/projects/gifti/ NIfTI: http://nifti.nimh.nih.gov/

It relies on external libraries: o Base64, by Peter J. Acklam: http://home.online.no/~pjacklam/ o miniz, by Rich Geldreich: http://code.google.com/p/miniz/ o dzip, by Michael Kleder: http://www.mathworks.com/matlabcentral/fileexchange/8899 o XMLTree, by Guillaume Flandin: http://www.artefact.tk/software/matlab/xml/ o mVTK, by Guillaume Flandin: http://www.artefact.tk/software/matlab/mvtk/

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: SPM: http://www.fil.ion.ucl.ac.uk/spm/

INSTALLATION

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 directoy containing @gifti is in MATLAB path:

addpath /home/login/matlab/gifti

Note that the handling of gzipped data requires Java, so you shouldn't start MATLAB with the '-nojvm' option and the following line must not return an error:

error(javachk('jvm'));

Alternatively, a C-MEX file can be compiled, see @gifti/private/zstream.c

TUTORIAL

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');

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GIfTI - a MATLAB GIfTI Library (v1.6)

INSTALLATION

TUTORIAL