[MINC-users] FDR analysis for cortical thickness

[Mishkin Derakhshan]

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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>>
>