> When you do the p->t conversion, are you assuming a two-sided t? You may have spotted my silly user error...
> Do you > want to try the --synth option (it's a lot easier when you *know* they > should be t). Yes. Thanks for your suggestions! +glenn > > > > [EMAIL PROTECTED] wrote: > >>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 >>> >>> >>> >>> >>> >> >> >> >> > > -- > 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
