Good point (meaning that I don't know the answer). I'll see if I can find out.
doug On Fri, 16 Oct 2009, Donna Dierker wrote: > Regardless: FDR's sensitivity appears resolution-dependent to me. > > On 10/16/2009 10:39 AM, Michael Harms wrote: >> 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 >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
