Gifti (.gii) is fundamentally different format from nifti (.nii) and there is therefore no straightforward way to map between them. Giftis work with vertices: points in a 3D space that form a 2D manifold, like the cortical sheet. Niftis work with voxel: 3D volumetric elements that span up a small volume. Niftis are 3D images, basically how they come from the scanner. For gifti's you need a cortical reconstruction that allows you to sample form 3D space to the 2D manifold.

I'd reccomend you take a look at the Freesurfer tutorial:

https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview

Also maybe take a look at pycortex:

https://gallantlab.github.io/

Does this post help?

https://www.mathworks.com/matlabcentral/answers/370862-how-to-convert-gii-files-to-nii

Walter Roberson posts:

• https://www.artefact.tk/software/matlab/gifti/ to do the reading.
• https://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image to do the writing.

There are several programs to convert MRI images. I use "MRIConvert", you can download it for free. You select your input data and where the program should export your converted .nii files.. done!

You may consider downloading the aedes software tool. It will help you to convert the images. Then if you wish, you can do a lot of other things with Fiji Image software.

All the best

Gaia Lapomarda did you find how to do this? I have the same problem and i didn't find a good program to convert gifti (MRIConvert or aedes don't support gifti files)..

Gifti (.gii) is fundamentally different format from nifti (.nii) and there is therefore no straightforward way to map between them. Giftis work with vertices: points in a 3D space that form a 2D manifold, like the cortical sheet. Niftis work with voxel: 3D volumetric elements that span up a small volume. Niftis are 3D images, basically how they come from the scanner. For gifti's you need a cortical reconstruction that allows you to sample form 3D space to the 2D manifold.

I'd reccomend you take a look at the Freesurfer tutorial:

https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview

Also maybe take a look at pycortex:

https://gallantlab.github.io/