Hello FreeSurfer experts, 

I just ran smoothing on a single 2D EPI image with a binary mask (that excludes NaN vertices), but it didn't seem work out well as the output image (e.g., test.mgh) contains zero values throughout vertices. 

 

Also, I've got two warning messages (see below): while one of which seems harmless (5311 NaNs), the other (ar=0 <=0) may be critical. 

If anyone has any idea/ suggestions, please help. 

-Glen 

mris_fwhm --hemi lh --s fsaverage_sym --mask mask.mgh --fwhm 4  --i rabold4_0065_sym_L.mgh --o test.mgh 

fsaverage_sym lh white

Number of vertices 163842

Number of faces    327680

Total area         61972.710938

GroupSurface 85910.812500

AvgVtxArea       0.378247

AvgVtxDist       0.693419

StdVtxDist       0.190498

WARNING: 5311 NaNs found in volume rabold4_0065_sym_L.mgh...

Loading mask mask.mgh

Found 158531 voxels in mask

Polynomial detrending, order = 0

Smoothing input by fwhm=4.000000, gstd=1.698644, niters=11 

Computing spatial AR1 

ar1mn = 0, ar1std = 0, ar1max = 0

avg vertex dist 0.693419

WARNING: ar1 = 0 <= 0. Setting fwhm to 0.

avg vertex dist 0.693419

fwhm = 0.000000