Interesting post Donna, but my understanding of FDR is that it sets the p-value threshold based on the LARGEST p-value that satisfies the FDR relationship.
That is, steps 3 and 4 in Genovese et al. (2002) are: 3) Let r be the largest i for which p <= i/V*q (assuming c=1) 4) Threshold the image at the p-value p(r). So, it isn't the case that you require the most significant p-value to satisfy p <= 0.05/V "just to get past i=1" as you put it in your post. Rather, you pick the largest p-value that satisfies the relationship, meaning that lower (more-significant) p-values may not have necessarily satisfied p <= i/V*q for their particular position in the sorted list of p-values. cheers, Mike H. On Fri, 2009-10-16 at 10:13 -0500, Donna Dierker wrote: > I never heard anything on my post here, but it might just be high > surface resolution: > > http://www.mail-archive.com/neuro-mult-c...@brainvis.wustl.edu/msg00026.html > > On 10/16/2009 09:58 AM, Michael Harms wrote: > > Your FDR analysis sounds correct. You probably have a rather small > > number of "marginally" significant vertices, which is why none survive > > FDR. You could try increasing the "q" value from say 0.05 to 0.1, in > > which case 10% of the surviving vertices would be expected to be false > > positives. > > > > cheers, > > Mike H. > > > > On Fri, 2009-10-16 at 12:03 +0200, Yulia WORBE wrote: > > > >> Dear Freesurfer team, > >> > >> We are currently doing a cortical thickness studies between a group of > >> psychiatric patients (n=60) and controls (n=30). We tested several > >> smoothing levels (15mm, 20mm, 25mm) > >> > >> When setting an uncorrected threshold (such as p<0.005), we obtained > >> several regions of decreased thickness, which are consistent with the > >> pathology. > >> > >> However, when trying to correct for multiple comparisons using FDR > >> ("Set Using FDR" button in qdec), the computed threshold is very high > >> (e.g. 4.3 for 20mm smoothing) and, obviously, no significant regions > >> are left. > >> > >> Did we do anything wrong in the analysis ? > >> > >> Thank you very much for your help, > >> Yulia > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
