FSL

# FDR - False Discovery Rate FDR User Guide |

## INTRODUCTION

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

The p image fed into fdr can be produced in a number of ways, for example:

- Output from 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`
        (this outputs the log(p) image)

      fslmaths logp1 -exp p1
        (this creates the p-value image)

      fdr -i p1 -m ../mask -q 0.05
       Probability Threshold is:
       0.00339819
        (this tells you the FDR threshold - p-values below 0.00339819 are significant)

      fslmaths p1 -mul -1 -add 1 -thr .99660181 -mas ../mask thresh_1_minus_p1
        (this creates a 1-p image for ease of display, thresholds that at
         1-thresh and then remasks)

  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.

- 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 is a p-value image from 0:1 where 1 is most significant (arranged this way to make display and thresholding simple). Therefore this needs to be inverted before feeding into fdr. Thus an example would be:

      fslmaths grot_vox_p_tstat1 -mul -1 -add 1 1_minus_grot_vox_p_tstat1
      fdr -i 1_minus_grot_vox_p_tstat1 -m mask -q 0.05

  This gives you the threshold that should be applied to the p-values. To view this, the easiest thing to do is take 1-threshold and threshold the original _vox_p_tstat1 image:

      fslmaths grot_vox_p_tstat1 -thr <1 - FDR threshold> thresh_grot_vox_p_tstat1

Copyright © 2005, University of Oxford. Written by S. Smith.