Hi-
I would loop over each hemisphere like there, rather than use the "both" file, because you would need to specify the hemisphere in the surface, anyways.
foreach hemi ( lh rh )
3dVol2Surf \
-spec std.141.TT_N27_${hemi}.spec \
-surf_A smoothwm \
-surf_B pial \
-sv TT_N27_SurfVol.nii \
-grid_parent sumMaps.nii.gz \
-map_func ave \
-f_steps 10 \
-f_index nodes \
-out_niml std.141.${hemi}.sumMap.niml.dset
# "-grid_parent .." should be a volume here
# you can also make the output a NIFTI directly, by including the suffix on the dset in "-prefix .."
# use "-sdata .." to provide the surface dataset that should be mapped into the vol
3dSurf2Vol \
-spec std.141.mySubj_both.spec \
-surf_A lh.smoothwm \
-surf_B lh.pial \
-grid_parent mySubj.nii \
-sv mySubj.nii \
-map_func ave \
-f_steps 10 \
-f_index voxels \
-sdata std.141.${hemi}.sumMap.niml.dset \
-prefix sumMapSubj_${hemi}.nii.gz
end
Note how you can output a NIFTI directly, above. You can add the two files to make a single NIFTI:
3dcalc \
-a sumMapSubj_lh.nii.gz \
-b sumMapSubj_rh.nii.gz \
-expr 'a+b*not(bool(a))' \
-prefix sumMapSubj_both.nii.gz
The reason the expression isn't just 'a+b', is juuust in case there is any overlap of nonzero values between the two volumetric datasets. By construction of the two hemispheric surfaces, I don't think there should be, but this should ensure that.
Though, just to note for future reference, to copy a BRIK/HEAD file to NIFTI, you can:
3dcopy FILE_NAME.HEAD FILE_NAME_NEW.nii.gz
The dataset you tried to convert with 3dAFNItoNIFTI wasn't actually a BRIK/HEAD dset, I guess, because the "-grid_parent .." being used wasn't a volumetric dataset.
How does that work?
--pt