nno / gifti

MATLAB GIfTI Library

GIfTI - a MATLAB GIfTI Library (v1.9)

https://www.artefact.tk/software/matlab/gifti/

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:

• 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:

• SPM: https://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 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

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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Copyright (C) 2008-2019 Guillaume Flandin [e-mail]