What is actually in the gii file? It is expecting only to read in overlay information (eg, a binary mask with values of 0 or 1 at each vertex). I have not used gifti all that much

On 3/4/19 10:55 AM, CAGNA Bastien wrote:

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Hi everyone, I need to convert a surfacic mask that is made from data of one subject projected onto fsaverage6 into a volumic map. To do so, I'm trying to use mri_surf2vol to take my Gifti file and create 3D version as Nifti file (using gray matter). So, I tryed this: mri_surf2vol --sd [subjects_dir] --subject fsaverage6 --o [output_filename].nii.gz --so [subjects_dir]/fsaverage6/surf/lh.white [lh.surf_mask_filename].gii --so [subjects_dir]/fsaverage6/surf/lh.white [rh.surf_mask_filename].gii

But it failed and tells me: MRISreadGiftiAsMRI: no overlay data found in file [lh.surf_mask_filename].gii

After quickly looking to the source code, at line 1077 of utils/gifti.cpp: //*-----------------------------------------------------------   MRISreadGiftiAsMRI() - reads GIFTI functional frames into   an MRI volume struct, which is a retro-fit usage to store   multiple frames of data (where in this case, a frame is one   complete vector of vertices).   This routine will only read NIFTI_INTENT_TIME_SERIES data   arrays. -----------------------------------------------------------*// I'm getting confused because (from what I understood) this function is trying to read gifti's data in a nifti and moreover i didn't find any example on the web of resampling Gifti file to Nifti image using mri_surf2vol. I think I missing some think but do not understand what.

Does any one have an idea about it?

Best regards, Bastien CAGNA

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