[MINC-users] FDR analysis for cortical thickness

[Jonathan Berken]

How do I open my list of t-values?

On Fri, Jun 8, 2012 at 2:35 PM, Mishkin Derakhshan <mishkind at gmail.com>wrote:

> On Fri, Jun 8, 2012 at 2:06 PM, Jonathan Berken
> <jonathan.berken at gmail.com> wrote:
> > Hi Mishkin,
> >
> > Thanks so much for your help!
> >
> > I already have R library and have ran cortical thickness analyses... I am
> > just not sure how to run the FDR analysis... I have the script from the
> > site, but not sure where to get the t-values from my results to input?
>
> So if you've ran the cortical thickness analyses, then you should have
> some t-values for whatever you tested for.
>
> In my example script, my array of t-values comes from here:
> vertexstatistics <- mni.vertex.statistics(glimfile, 'y ~ group',
> vertex.table=datatable)
>
> vertexstatistics contains a lot of different items, the array of
> t-values are here:
> vertexstatistics\$tstatistic[,2]
>
> The t-values represent the result of a two-tailed t-test for the test
> y ~ group, which usually means you are testing for differences in
> cortical thickness (y) in the different groups (ie. francophones vs.
> anglophones). What 'y' and 'group' actually mean, depend on what you
> put in your glim file, but if you've ran your analysis already then i
> have a feeling you know this already.
>
> > Can
> > I run the FDR after I do my initial CT regression?
>
> Sorry, but I don't actually know what you mean by initial CT
> regression? I use MRI data, and I don't actually look for differences
> in cortical thickness but just use the library for other vertex wise
> tests that I need. Like Jason said though, the FDR can be calculated
> on any array of t-values (or pvalues) that are the output of anything
> you are trying to test for.
>
> If you look at the code (in R type: 'library(mni.crotical.statistics)'
> then 'mni.compute.FDR') you can see that it actually needs p-values,
> but it can compute those from the given t-stats if you give it the
> degrees of freedom.
>
> >
> > Jonathan
> >
> > On Fri, Jun 8, 2012 at 2:00 PM, Mishkin Derakhshan <mishkind at gmail.com>
> > wrote:
> >>
> >> Hi Jonathan,
> >>
> >> At the risk of depriving you hours of endless fun coding this up
> >> yourself, attached is my implementation using the
> >> mni.cortical.statistics library (which you will need to install).
> >>
> >> There is quite a bit of documentation on the bic wiki:
> >> http://wiki.bic.mni.mcgill.ca/index.php/ThicknessStatistics
> >>
> >> I'm at wb319 in the bic if you need help.
> >> mishkin
> >>
> >> p.s this is how to install the R library (using a bash shell) if you
> >> didn't know:
> >> 1. download the mni.cortical.statistics library
> >> 2. R CMD INSTALL --library=/path/to/useful/extra/libraries/for/R/
> >> mni.cortical.statistics
> >> 3. export R_LIBS=/path/to/useful/extra/libraries/for/R/
> >>
> >>
> >> On Fri, Jun 8, 2012 at 11:19 AM, Jason Lerch <jason at phenogenomics.ca>
> >> wrote:
> >> > There's an implementation in mni.cortical.statistcs and RMINC as well
> as
> >> > Keith's matlab surfstats.
> >> >
> >> > The recipe in R:
> >> >
> >> > 1) create a vector of p-values
> >> > 2) qvals <- p.adjust(pvalues, "fdr")
> >> >
> >> > Jason
> >> >
> >> > On 2012-06-08, at 11:15 AM, Jonathan Berken wrote:
> >> >
> >> >> Hello,
> >> >>
> >> >> I was wondering if someone who is familiar with FDR analysis for
> >> >> cortical
> >> >> thickness might be able to help me work out the script.
> >> >>
> >> >> Thanks!
> >> >>
> >> >> Jonathan
> >> >> _______________________________________________
> >> >> MINC-users at bic.mni.mcgill.ca
> >> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >> >
> >> > _______________________________________________
> >> > MINC-users at bic.mni.mcgill.ca
> >> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >> _______________________________________________
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> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >
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