FDR is based on the data, so you can't really say that a voxel-wise threshold is low or high. But 1x10^04 is actually not too bad, considering that the bonferonni thresh would be about 3x10^-7. The jump you see is not entirely unexpected, but I'm going to have to refer you to the FDR liturature (or Tom Nichols:) to get a deeper explanation.

The new tools that I am working on will use clustering to help reduce the multiple correction penalty. Should be ready in the next couple of weeks.

doug




Sasha Wolosin wrote: 
When I set FDR = .05, or anything under .85, and select "set threshold
using FDR" the min threshold is always set to 4.03, which is about p=
.0001, correct?  Would you normally require such low p-values for this
type of analysis?  Why would such varied FDRs result in the same min
threshold?  We do not see any results when the min>2.0 (p=.01), so this
is very problematic for us.  Also, at just over FDR = .85 (I realize
this is absurdly high) the min threshold jumps down to 1.23, do you have
any idea why this jump might occur?
Thanks,
Sasha


  
Bruce Fischl <fischl@nmr.mgh.harvard.edu>  >>>
        
.05 is fairly standard I think.
On Mon, 9 Jan 2006, Sasha Wolosin wrote:

  
Is this something you apply frequently at MGH?  What FDR value would
    
you
  
typically require?

    
Doug Greve <greve@nmr.mgh.harvard.edu>  >>>
          
Currently, mris_glm does not attempt to correct for multiple
comparisons, though this feature will be in the next release. In the
mean time, you can correct for multiple comparisons using FDR in
tksurfer.



Sasha Wolosin wrote:

    
Dear all,
 I would like to learn more about group analysis using mris_glm.  How
does the program correct for the problem of multiple comparisons?  Is
there any way to determine the rate of false positives?
Thanks,
Sasha

Sasha Wolosin
Research Assistant
Developmental Cognitive Neurology
Kennedy Krieger Institute
707 N. Broadway
Baltimore, MD 21205
ph: (443) 923-9270
wolosin@kennedykrieger.org



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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422