Thanks Doug. Yes, it works well now! -Glen
On Thu, May 23, 2013 at 1:50 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > 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 > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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 > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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