The t is computed as the signed square root of the F (not Fsig) volume: t.vol = sqrt(Fvol.vol) .* sign(ces.vol);
The Fvol (and do t) is not computed from the sig (the other way around). Are you sure that the t-value does not look right in those areas? doug Qi Zhu wrote: > 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. >> >> > > > -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
