Wei-Chung,

Below is the response from Satoru Hayasaka in our group on your
dilemma...



So, Ben gave me a list of t-scores for this ROI, and I was able to
figure out why this person got strange results. As I said yesterday, the
FDR threshold is determined by plotting uncorrected p-values from the
smallest to the largest. Then you draw a straight line corresponding the
FDR value of your choice (0.05, 0.072, etc), and wherever the p-value
curve crosses this straight line is the FDR threshold. See the attached
figure for an illustration of this. 

Now, in order for the FDR threshold to exist, the p-value curve should
start below the straight line, and crosses the straight line as it
increases. Unfortunately, this person's p-value curve doesn't start
below the straight line, so theoretically the FDR threshold is
undefined, and nothing survives the FDR correction. But this person
played with the FDR threshold value to cause a double-crossing (see
yellow line). This, in no way, makes the FDR-corrected p-values valid;
this FDR-threshold "fooled" (hopefully unintentionally) spm_P_FDR.m and
made it produce invalid p-values. I guess whoever wrote spm_P_FDR.m
wasn't prepared for a scenario like this. 

So, this is the answer to this conundrum. Nothing really survived; but
this person tweaked the threshold and produced the results which are
invalid and misleading. So, I guess you have to call a spade a spade.
Nothing survived at FDR<0.05, and that's the end of the story. It has
nothing to do with PickAtlas. 

-Satoru



------------------------------------------------------------------------
Joseph A. Maldjian, MD
Professor and Chief of Neuroradiology
Director Advanced Neuroscience Imaging Research Core (ANSIR)
Wake Forest University School of Medicine
Office:336 716-2815
fax:    336 716-2870
email: [log in to unmask]
website: www.fmri.wfubmc.edu/maldjian.htm
------------------------------------------------------------------------
-

-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
On Behalf Of Wei-chun Wang
Sent: Monday, February 09, 2009 7:38 PM
To: [log in to unmask]
Subject: [SPM] wfu pickatlas problem?

I'm trying to use pickatlas with SPM and I'm running into a problem. I
have
a ROI that appears to be just under the threshold for significant after
small volume correction (.049 FDR). However, when I use pickatlas and
.05
FDR as my threshold, my activation does not reach threshold. HOWEVER, if
I
use .072 FDR my activations show up, and in the table the corrected p
value
is properly listed as .05
To sum, my problem is that the threshold has to be relaxed by ~.022 in
order
for the actual threshold (.05) to be seen by SPM.

I've included 3 screen shots that illustrate my problem:
"uncorrected" shows what happens if i set an uncorrected p-value and
then
use SPM's SVC function. you can see that the FDR corrected is .05
"pickatlas_05" shows what happens if i use pickatlas and set the p-value
to
.05 FDR. no activations reach the threshold
and finally, "pickatlas_072" shows what happens if i use pickatlas and
set
the p-value to .072 FDR. at this point it appears most of the
activations
that reach the .05 threshold appear.

This isn't a rounding error. The activations do not show up if I try
.051 or
.06, only at .072. Also matlab shows that the FDR corrected p-value is
~.049. I was wondering if this is a bug in the software and if there is
a
workaround? Or is it a problem in my data? I was hoping to use this
program
in order to produce accurate activation maps of just the small volume
corrected ROI. So alternatively, if anyone can recommend a separate
method
for doing so I would be quite appreciative.
Wei-chun Wang