Dear Doug, Thanks very much for your prompt response. I tried what you suggested and the sig map looks fine now, that's probably the best that we can get for the sig map, because of the limitation of the MATLAB I guess. But for the t map, the values are still not correct for those voxels that highly activated, because they're just calculated based on the sig values, and they can only go up to 17.98 in my case because of the limitation. And I am also quite confused by the way that selxavg3 calculated the t values, which are calculated as the square root of Fsig values, but not the F values. Is that correct?
Best, Qi Zhu, PostDoc Laboratorium voor Neuro- en Psychofysiologie K.U.Leuven Medical School Herestraat 49, B-3000 Leuven (Belgium) phone +32 16 33 02 09 On Tue, Dec 20, 2011 at 8:54 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > I think this is due to the high DOF and probably high t-value causing the > significance in matlab to be computed as 0. This gets converted to Inf > (infinity) when the -log10(p) calculation is made, then the Inf gets set to > 0 when the volume is saved. The quick fix for you is to change > fast_selxavg3.m (in $FREESURFER_HOME/fsfast/toolbox). There is a single line > that reads: > > fsigmat = -log10(pmat) > > change this to > > fsigmat = -log10(pmat + eps(0)); > > Let me know if this works and I'll update our source code. > > doug > > > > > > Qi Zhu wrote: >> >> Dear Doug, >> >> I used selxavg3-sess in freesurfer 5.0 to run a big GLM analysis on a >> monkey data set containing 147 runs. But When I check the results, I >> found that in the voxels where the t-values should be very high were >> turned out to have a value of zero. I checked the brainmask, the ces >> and the cesvar values, they all look fine. It seems that only the ces >> values in these voxels are a bit high compared to the nearby normal >> voxels (e.g. 1.17 (ces)/0.00048(cesvar) compared to 0.74/0.00040 in a >> nearby normal voxel). And it seems that not only me have this problem >> (similar problem posted in the mailinglist before. >> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13789.html). >> Do you know what the problem would be and how to solve it? Thanks very >> much for your help. >> >> Attached please find an image of the problem. >> >> Best, >> >> Qi Zhu, PostDoc >> Laboratorium voor Neuro- en Psychofysiologie >> K.U.Leuven Medical School >> Herestraat 49, B-3000 Leuven (Belgium) >> >> ------------------------------------------------------------------------ >> > > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
