[MINC-users] Calculating an FDR threshold

[Mishkin Derakhshan]

Hi Jennika,

I've never used glim_image or fMRIstat, but I have computed FDR
thresholds using R and the mni.cortical.statistics library.

If you can get the VBM t-stat map that is generated from glim_image,
into a simple text file listing each t-stat per row, then you can use
the following:

1. Install R and library
on ubuntu: sudo apt-get install r-base-core
then download the mni.cortical.statistics library to /tmp/
http://www.bic.mni.mcgill.ca/users/mishkin/files/mni.cortical.statistics.0.9.0_patched.tar.gz
cd /tmp
tar xvzf mni.cortical.statistics.0.9.0_patched.tar.gz
mkdir /home/mishkin/R_LIBS (or wherever you want to keep your R libraries)
R CMD INSTALL --library=/home/mishkin/R_LIBS/ mni.cortical.statistics
export R_LIBS=/home/mishkin/R_LIBS

2. Calculate the FDR in R
R
library(mni.cortical.statistics)
tstats =scan("my_file_of_tstats.txt")
q <- mni.compute.FDR(tstats, df=12, fdr=0.05)
write(q,"fdr_threshold_output.txt",1)

where:
"my_file_of_tstats.txt" looks like this:
-2.23
-2.24
...
-1.93
0.32

"df = 12" means 12 degrees of freedom. usually the N of each group -2
"fdr = 0.05" means use an fdr threshold of 0.05

"fdr_threshold_output.txt" will be an output file containing a number
that indicates the fdr threshold t-stat:
-2.1

So, this would mean that all t-stats less than -2.1 would be deemed
significant using an FDR of 0.05.

hth,
mishkin


On Tue, Sep 27, 2011 at 9:04 PM, Jennika Soles <jennika.soles at gmail.com> wrote:
> Hi All,
>
> Does anyone know if there is a particular method of calculating an FDR
> threshold for a VBM t-stat map generated using glim_image? Would using the
> tool in fMRIstat be acceptable?
>
> Thanks!
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>