Hi,
Did you get nothing for both pID and pN in FDR.m ?
Can you run your fdr command with the -v option and send us
the output? I'd also like to know the size of the mask (fslstats with
-V
will tell me what I want to know).
As your threshold is very low, I'm assuming that not much passes
this, but I cannot quite see why the results are different.
All the best,
Mark
On 17 Sep 2009, at 01:58, Jason Stein wrote:
> Hello FSLers,
>
> I have a question regarding the FSL fdr command.
>
> First, I created a map of P-values from a program outside of FSL
> which does a multiple linear regression. Then, I created a
> histogram of the P-values within a mask of interest. This
> histogram is not attached due to space limits (my previous email was
> rejected). A description is that there are many voxels with high P-
> values and fewer voxels with low P-values (a left half frowning
> histogram). Then, I ran two FDR corrections. (a) Taking only the P-
> values within the mask using Matlab I used the FDR.m script from Tom
> Nichols' website, and (b) The fdr command in FSL.
>
> Method (a) gave me no P-value that passes the FDR at a q-value of
> 0.05 using the standard Benjamini Hochberg 1995 FDR method.
> However, method (b) gave me a P-value threshold - it did pass.
> Considering that the histogram looks the opposite of what I would
> expect for passing FDR and that methods (a) and (b) give different
> results, I'm confused as to what's going on. Can someone help?
>
> Also, the histogram of P-values we were studying were created by
> studying FA differences using standard parametric regression. Is
> the reason the histogram looks funny (in that a null histogram
> should be flat, not having fewer voxels with less significance)
> because we are not satisfying the distributional assumptions of a
> parametric regression? In other words, should we be using non-
> parametric regression?
>
> Thanks in advance for any help,
> Jason Stein
>
>
>
> fdr -i /Users/M/Desktop/Stats/Output_stats/EFFECT_V/
> VolumeRegressionAnalysis.OutputP-values_0-2.img -m /Users/M/Desktop/
> Stats/Mori_mask_WM_stats_220.img -q 0.05
> Probability Threshold is:
> 0.000392611
>
>
>
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