Dear Freesurfer experts, I ran recon-all with the flag -qcache to generate smoothed cortical thickness maps. In order to check how the flag "-qcache" is smoothing the cortical thickness data. I looked into the file $subj_dir/scripts/recon-all.log" which showed that the following command was applied:
mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5--sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm5.fsaverage.mgh --cortex
Please I want to know whether the flag "--fwhm" applies similar smoothing method to the smoothing output of the command "fslmaths":
fslmaths <input_image.nii> -kernel gauss 2.213 -fmean <output_image.nii> -odt float
I want to smooth two different modality-images using the cortical thickness smoothing method.
Thank you for any advice! John