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Hi freesurfer experts,
I'm dealing with an issue with smoothing on surface data that unfortunately contain 'NaN' in the ventral temporal region (which is a region that we are interested in).
This may be due to the slab data acquisition, where the bottom of the slice meant to be at the bottom of the tomporal lobe for every subject. Apparently, we didn't quite succeed in this as we saw missing data points that are filled with 'NaN' during 2D reconstruction in some subjects' 2D data.
In the cartoon above, the yellow color depicts vertices with 'NaN' in the ventral temporal region , and you can easily see how this is affected by smoothing (4mm FWHM), such that a large swath of ventral regions have NaNs after smoothing.
I've tried smoothing both with and without --cortex flag, but the results were the same regardless.
So, the best bet would be masking out those NaN vertices before smoothing and I wonder if there is any way of doing it in freesurfer. Otherwise, I may need to consider smoothing outside of the freesurfer using Matlab (but I have no experience about this approach).
If anyone has previously dealt with this issue (hope I'm not the only one) and know how to get around with it either inside or outside of the freesurfer, please help me. -Glen
