btw, if you simply "touch" the contrast mat files in the analysis directory, it will only regenerate the contrasts. That should save you some time because it won't have to re-run all of selxavg. doug
Douglas N Greve 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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.
