Hi Glen, if it is just a slab, you are probably smoothing in a bunch of 0s. Try smoothing only the areas within a mask of the slab. You can do this by passing a label to mri_surf2surf ( you can also create a mask and pass it to mris_fwhm). doug On 05/13/2013 10:12 AM, Glen Lee wrote:
Inline image 3Dear freesurfer expert
I've tried both relatively small and large size of smoothing kernel (i.e., 4mm vs. 10mm) on the surface EPI data using mri_surf2surf function (e.g., mri_surf2surf --hemi lh --s fsaverage_sym --fwhm )
Attached are displays of raw EPI, 4mm, and 10 mm FWHM. As can be seen, the areas being smoothed by 10mm FWHM is quite off from those in the raw 2D EPI whereas 4mm result looks reasonable.
If anyone has some intuition about why this happened, please help me. -Glen ps) the area with colors show vertices with non-zeros values (also it was reconstructed from slap EPI)
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