Hi Doug and Sebastian, thanks for your input. I think I can confirm that it is the problem that Sebastian described. FS 5.1 uses betainc, which returns 0, even in Matlab R2011b. The workaround that Sebastian suggested works, with a slight modification. In line 888 in fast_selxavg3.m currently reads ind = find(pmat == 0); pmat(ind) = 1; That seems wrong to me, as -log10(1) gives 1. I replaced line 888 with ind = find(pmat == 0); pmat(ind) = eps(0); -log10(eps(0)) gives 323.3062. Sebastian's solution of pmat(ind) = eps underestimates the significance because eps is by default eps(1). Does that make sense?
I confirmed that the time courses indicate a highly significant difference; I have 27 runs of block design; the problem happens both for contrasts against baseline and for contrasts between conditions; I currently have this problem only in one subject. Thanks, Caspar 2012/11/29 Sebastian Moeller <sebastian.moell...@rwth-aachen.de>: > Hi Doug, hi Caspar, > > which matlab version are you using? We had some issues in the past that some > matlab 2007 and 2009 statistics toolbox versions returned p values of 0, > which obviously will not work as overlay, since those typically assume a > volume of: > -log10(p_value) > and on matlab 2007b (maci): >>> -log10(0.0) > ans = > Inf >>> -log10(eps) > ans = > 15.6536 > So you should > > So test your input stat volumes for 0.0 and try to replace those with eps in > matlab and see how the overlay look then. Then try to teach fs-fast to do > this automagically :) > For saity checking have a look at the time course at those voxels (I assume > NHP block design data here), and remember if you can see the modulation in > the time courses with your bare eyes it will most likely be significant. So > at those voxels where the contrasts return zero I would expect really great > time courses with strong differences in modulation hiught between the members > of the -a and -c collections of contrast blocks. > > best > Sebastian > > > On Nov 29, 2012, at 09:55 , Douglas N Greve wrote: > >> >> Oh, I did not realize this was an fsfast issue, I thought you were using >> mri_glmfit. In that case, I'm not sure what could be causing the problem >> since the p-values are being computed by matlab. How many runs do you >> have? Is is a contrast that has a huge amount of power(eg, something vs >> fixation)? Does it happen in other subjects? One path to debugging is to >> run selxavg3-sess with -run-wise. This will create an analysis for each >> run separately. You can then see whether one run in particular is >> causing the problem. >> doug >> >> On 11/27/2012 08:34 PM, Caspar M. Schwiedrzik wrote: >>> Hi Doug, >>> I am afraid the p values are still too small in Free Surfer >>> Linux-centos4_x86_64-stable-pub-v5.1.0-full. >>> I redid >>> mkanalysis-sess >>> mkcontrast-sess >>> selxavg3-sess >>> in 5.1., it looks verz similar as in 4.5., including a whole of 0.0 in >>> the center of the cluster. >>> Any further advice? >>> Thanks, >>> Caspar >>> >>> >>> >>> 2012/11/26 Douglas Greve <gr...@nmr.mgh.harvard.edu>: >>>> No, it does not. With version 5 I went to a simple AR1 model instead. >>>> doug >>>> >>>> >>>> >>>> On 11/26/12 10:34 PM, Caspar M. Schwiedrzik wrote: >>>>> Hi Doug, >>>>> thanks for the input. What I meant is that in version 5.1, >>>>> mkanalysis-sess does not seem to recognize the -taumax flag to set the >>>>> maximum delay for the autocorrelation function. >>>>> Caspar >>>>> >>>>> >>>>> 2012/11/26 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: >>>>>> >>>>>> On 11/26/2012 02:12 PM, Caspar M. Schwiedrzik wrote: >>>>>>> Hi Doug, >>>>>>> I'll do that. >>>>>>> Two quick follow-up questions regarding 5.1: >>>>>>> - it seems that I cannot specify taumax anymore in mkanalysis-sess. Is >>>>>>> there another argument that would allow me to set the autocorrelation? >>>>>> What do you mean by "set the autocorrelation"? You can turn it off with >>>>>> -no-whiten. >>>>>> >>>>>>> - in a block design, would refeventduration be the block length or the >>>>>>> length of the individual events within a block? >>>>>> The block length. This will not change the p-values, only percent signal >>>>>> change values (often not even looked at). >>>>>> doug >>>>>> >>>>>>> Thanks, >>>>>>> Caspar >>>>>>> >>>>>>> 2012/11/26 Douglas N Greve<gr...@nmr.mgh.harvard.edu>: >>>>>>>> Hi Caspar, I think I fixed this in later versions. If you upgrade, you >>>>>>>> can run the stats from 5.1 with recons from 4.5 (just don't mix recons >>>>>>>> from different versions). >>>>>>>> doug >>>>>>>> >>>>>>>> On 11/26/2012 01:15 PM, Caspar M. Schwiedrzik wrote: >>>>>>>>> Hi! >>>>>>>>> I ran into a funny problem when calculating contrasts in Freesurfer >>>>>>>>> 4.5.0. >>>>>>>>> Namely, the center of my cluster of significant voxels has a p-value >>>>>>>>> of -0.0, resulting in a funny whole where you would otherwise expect >>>>>>>>> to find the most significant voxel(s). >>>>>>>>> It seems that the p-value is too small. Is there a workaround >>>>>>>>> available? >>>>>>>>> Thank you very much, >>>>>>>>> Caspar >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> >>>>>>>>> >>>>>>>> -- >>>>>>>> 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 >>>>>>>> Outgoing: >>>>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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. >>>>>>>> >>>>>> -- >>>>>> 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 >>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>> >>> >> >> -- >> 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 >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Sebastian Moeller > > telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 > fax: 626-395-8826 > German GSM: +49 - 15 77 - 1 90 31 41 > mobile: +1-626-325-8598 > +1-626-807-5242 > US CDMA: +1-626-807-5242 > moel...@caltech.edu > > Division of Biology > MC 114-96 > California Institute of Technology > 1200 East California Boulevard > CA 91125, Pasadena > USA > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
