The second error just means that it cannot compute the fwhm. This will
go away if you add --smoooth-only.

On 05/23/2013 01:31 PM, Glen Lee wrote:
> 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
>
>
>

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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