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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 [email protected] 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.
