Hi Afni Experts,
I was having an issue with converting all of my surface files from freesurfer to SUMA format. I wanted to see what are the manual commands necessary for a group analysis in case i cannot get suma_make_spec_fs working with my files (or what I need to modify).

I have a subjects native files in FS/mri and FS/surf folder.

Using the -qcache option I also have created the thickness files which are smoothed and warped to fsaverage (lh.thickness.fwhm10.fsaverage.mgh). These are present in the FS/surf folder along with the subject space files. I used AFNI's @SUMA_Make_Spec_FS command to convert my subject's fsaverage thickness files to SUMA format.


I want to use the following:
cd FS1/
@SUMA_Make_Spec_FS -sid FS1 -GNIFTI

This would convert all of my subject files to afni format and aligned to the original input (with potential of half voxel shift on odd slices as I later read). This created the orignal surfaces and ran mapsiconahedron however the lh.thickness.fwhm10.fsaverage.mgh files were not converted or run through MapIconsahedron.

1) For a group analysis are only the brain surfaces converted via mapicosahedron, or also each individual thickness file?

2) Is there a way to take the files lh.thickness.fwhm10.fsaverage.mgh located within the subject FS/surf and run through @SUMA_Make_Spec_FS where the surface is specified for fsaverage since lh.thickness.fwhm10.fsaverage.mgh is already warped to fsaverage?

Or do you recommend I just run something like the following instead for left and right hemisphere? Please correct if mistakes below.

mkdir FS1/SUMA
mris_convert -c ./FS1/surf/lh.thickness.fwhm10.fsaverage.mgh \
$SUBJECTS_DIR/fsaverage/surf/lh.white \
FS1/SUMA/FS1.lh.thickness.fsaverage.gii

MapIcosahedron -spec $SUBJECTS_DIR/fsaverage/SUMA/fsaverage_lh.spec -ld 141 -dset_map FS1/SUMA/FS1.lh.thickness.fsaverage.gii -prefix std.141.FS1_fsaverage_lh.spec

inspec -LRmerge $both ${ldpref[$ild]}fsaverage_lh.spec


Thanks,
Ajay