sorry, -log10(1) gives 0 of course. caspar 2012/11/30 Caspar M. Schwiedrzik <cschwie...@rockefeller.edu>: > 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 >>
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