Yes, seems weird. The image that I attached to you in the first mail is actually a t map, so the t value in those areas are also zero. And according to what I read from fast_selxavg3.m, the t value is actually calculated from the fsig, which is: t.vol = sqrt(fsig.vol).*sign(ces.vol), and fsig.vol is calculated from the p value that came from the Ftest. So the t value is calculated wrong in fs 5.0. I am now changing this line to:
Fvol = fast_mat2vol(Fmat,mri.volsize); t.vol = sqrt(Fvol).*sign(ces.vol); Is this correct? Best, Qi Zhu, PostDoc Laboratorium voor Neuro- en Psychofysiologie K.U.Leuven Medical School Herestraat 49, B-3000 Leuven (Belgium) On Wed, Dec 21, 2011 at 5:31 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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
