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