Research Overview

fdr is a simple program which takes in a p-value image and uses FDR ( False Discovery Rate ) theory to carry out multiple comparison correction. For detail on FDR theory see Tom Nichols' FDR page.




The p-value image fed into fdr can be produced in a number of ways.

Use with FEAT

Change directory into the stats subdirectory. It is then necessary to convert a give cope and varcope image into a p-value image. For example:

ttologp -logpout logp1 varcope1 cope1 `cat dof`

fslmaths logp1 -exp p1

fdr -i p1 -m ../mask -q 0.05

fslmaths p1 -mul -1 -add 1 -thr .99660181 -mas ../mask thresh_1_minus_p1

Note that if you are looking at a cope created by FLAME fixed-effects, the correct dof is not in the "dof" text file, but in the tdof_t1 image.

Use with randomise

Output from randomise can be fed directly into fdr; use the voxel-based thresholding, uncorrected for multiple comparisons, i.e. a *_vox_p_tstat* image. This images stores values as 1-p rather than p (where p is the p-value from 0 to 1). That is, 1 is most significant in a 1-p image (and it is arranged this way to make display and thresholding simple). Therefore fdr needs to know that it is a 1-p image. Thus an example would be:

fdr -i grot_vox_p_tstat1 --oneminusp -m mask -q 0.05 --othresh=thresh_grot_vox_p_tstat1

where the input image, grot_vox_p_tstat1, contains 1-p values, as output by randomise. Note that the name of this image should be changed to whatever you have called your image.

The output from fdr gives you a p-value threshold (not a 1-p value) that can be applied to the p-values, as well as a thresholded image, thresh_grot_vox_p_tstat1, where all non-significant voxels are given a value of 1-p=0 and significant voxels still contain the original 1-p values.

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FDR (last edited 17:02:31 29-07-2016 by AndersonWinkler)