Actually, it is an excellent question, and gets at the heart of my research-- rather than saying all bets are off, using the skew of the t-values to gauge the effect (or number of hypothesis/vertices where we have an effect).
My big problem is that I can't investigate the distribution of the t-values if I don't know which set of t-values is valid. Converting p to t should give me the same t-values as the output t-values, but it doesn't, not even close. +glenn > This might seem like an odd question, but why do you expect the t values > to be t-distributed? Remember, they will only be t-distributed under the > null. If you have an effect, and I assume you do, then all bets are off. > Try doing the same thing with synthetic guassian noise (mri_glmfit will > do this for your if you just add --synth to the cmd line). > > doug > > [EMAIL PROTECTED] wrote: > >>Hi, >> >>I'm seeing some odd behavior in t-values and p-values exported from >>FreeSurfer. In geeky detail: >> >>fit a linear model using FreeSurfer, saving t and p-values >>convert output files to ascii >>load ascii files into R >>convert the FreeSurfer "p-values" into real p-values via >>lh.pval <- 10^(-1*abs(freesurfer.lh.pvals)) >># this is necessary as FreeSurfer writes the -log10 of the pvalue, with >>the sign >># demonstrating direction of effect. >>convert these pvalues to tvalues >>lh.convert.t <- qt(lh.pval,XX) # where XX is the degrees freedom >> # I have several studies, 60 < XX >>< 200 >>A histogram of lh.convert.t is roughly OK, could be zero-mean. >> >>HOWEVER, >>the t-values exported by FreeSurfer are not. In one study, the range of >>the converted t-values was [-3.8, 3], but the range of the raw t-values >>was [-0.6,3.8]. In a second study, the range of the raw t-values was >>[0,17]. >>As you could guess from these ranges, histograms of the two versions of >>t-values also differ radically. >> >>Regarding version numbers and such, I have three experiments I have >>checked for this phenomenon. Two are old, and were run using version 1.2 >>(output files in .w format, etc), and the third study is new (version >> 3.X, >>outputs are F.mgz and sig.mgz). We run the linux/RHEL versions. >> >>My questions: why are the t-values output by FreeSurfer so oddly >>distributed? and why don't they agree with what i get when I convert the >>p's to t's? Silly user error on my part? >> >>Thanks much for any insights >> >> >>_______________________________________________ >>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 > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > -- -------------------------------------- I'm only in it for the glory. Glenn Lawyer +352 661 967 244 Instituttgruppe for psykiatri Seksjon Vinderen PB 85 Vinderen 0319 Oslo http://folk.uio.no/davidgl _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
