I would be interested in this as well. -Derin
On Oct 16, 2009, at 11:40 AM, Doug Greve wrote: > > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
