Yes that is correct. That was fixed with version 5.1 so current distributions do the right thing. doug
Qi Zhu wrote: > 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 >> >> > > > -- 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
