https://github.com/gllmflndn/gifti
MATLAB/Octave GIfTI Library
https://github.com/gllmflndn/gifti
gifti matlab neuroimaging neuroscience octave
Last synced: about 2 months ago
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MATLAB/Octave GIfTI Library
- Host: GitHub
- URL: https://github.com/gllmflndn/gifti
- Owner: gllmflndn
- License: mit
- Created: 2018-07-18T08:50:56.000Z (about 8 years ago)
- Default Branch: main
- Last Pushed: 2025-03-10T11:48:54.000Z (over 1 year ago)
- Last Synced: 2025-03-10T12:30:01.586Z (over 1 year ago)
- Topics: gifti, matlab, neuroimaging, neuroscience, octave
- Language: C
- Homepage: https://www.gllmflndn.com/software/matlab/gifti/
- Size: 1.01 MB
- Stars: 25
- Watchers: 2
- Forks: 13
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# GIfTI library for MATLAB/Octave
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This GIfTI library allows to handle the GIfTI Geometry file format from the Neuroimaging
Informatics Technology Initiative (NIfTI) using a MATLAB/Octave class:
* GIfTI: https://www.nitrc.org/projects/gifti/
* NIfTI: https://nifti.nimh.nih.gov/
It relies on external libraries:
* [yxml](https://dev.yorhel.nl/yxml), by Yoran Heling
* [Base64](https://stackoverflow.com/a/37109258), by polfosol
* [miniz](https://github.com/richgel999/miniz), by Rich Geldreich
Note that these tools are already included in the GIfTI library provided
here, so you don't need to install them separately.
There are import facilities from [FreeSurfer](https://surfer.nmr.mgh.harvard.edu/fswiki/FileFormats),
[VTK](https://vtk.org/), [Wavefront OBJ](https://www.wikipedia.org/wiki/Wavefront_.obj_file),
[Stanford PLY](https://www.wikipedia.org/wiki/PLY_%28file_format%29),
[STL](https://www.wikipedia.org/wiki/STL_%28file_format%29) and
[MZ3](https://github.com/neurolabusc/surf-ice/tree/master/mz3) file formats.
There are export facilities to [VTK](https://vtk.org/),
[Collada](https://www.khronos.org/collada/),
[IDTF](http://www.meshlab.net/),
[Wavefront OBJ](https://www.wikipedia.org/wiki/Wavefront_.obj_file) and
[JS/JSON](https://plot.ly/javascript/) (for [Plotly](https://plot.ly/javascript/)) file formats.
This library is also part of [SPM](https://www.fil.ion.ucl.ac.uk/spm/).
## INSTALLATION
[MATLAB](https://www.mathworks.com/products/matlab.html) R2007a or above is required to use most of the features of
this toolbox. [GNU Octave](https://www.octave.org/) is also supported.
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:
```matlab
addpath /home/login/Documents/MATLAB/gifti
```
The library relies on a number of C-MEX files (`zstream`, `base64`, `xml_parser`).
Compiled versions for 64 bit MATLAB on Windows, Linux and Mac are provided
but they can easily be compiled by yourself otherwise, see `@gifti/private/Makefile`.
## TUTORIAL
In the following, we use the files contained in `BV_GIFTI.tar.gz` (BrainVISA examples),
available from the [NITRC website](https://www.nitrc.org/frs/?group_id=75&release_id=123):
```matlab
% Read the GIfTI surface file
g = gifti('sujet01_Lwhite.surf.gii')
% Read the GIfTI shape file
c = gifti('sujet01_Lwhite.shape.gii')
% Display mesh
figure; plot(g);
% Display mesh with curvature
figure; plot(g,c);
```
In a similar way, a `gifti` object can be created from an extracted isosurface from volume data and saved to a file:
```matlab
load mri % an example dataset available in MATLAB
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');
```
## SEE ALSO
[Export to Plotly](https://gllmflndn.github.io/gifti/).