Mike (and Jorge),
Thanks! yours, LMR > Subject: [Fwd: Re: [Freesurfer] setting of fdr thresholds in qdec] > From: mha...@conte.wustl.edu > To: freesurfer@nmr.mgh.harvard.edu; lari...@gmail.com > Date: Thu, 25 Jun 2009 10:08:05 -0500 > > > Lars, > I had a similar question regarding the setting of the FDR p-value > threshold back in Dec 2008 (search "fdr Harms" in the Archive), but for > some reason, I see that Nick's reply to me didn't make it into the > archive, even though he cc'ed the FS list. > > So, I'm forwarding Nick's response below, which I believe answers your > question. > > cheers, > -Mike H. > > -------- Forwarded Message -------- > From: Nick Schmansky <ni...@nmr.mgh.harvard.edu> > To: Michael Harms <mha...@conte.wustl.edu> > Cc: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] setting of fdr thresholds in qdec > Date: Tue, 16 Dec 2008 18:06:24 -0500 > Mike, > > I've attached the code that operates the "Set Using FDR" button in qdec. > > First have a look at the routine SetSurfaceScalarsColorsUsingFDR in > vtkQdecWindow.cxx, which calls our FDR library and returns a threshold. > Then, it calls the routine SetSurfaceScalarsColors after setting mid = > threshold + 1.5, and max = threshold + 2.25. from there, > SetSurfaceScalarsColors just checks min, mid and max against the current > values (from prior run) and updates them if they differ. so basically, > the 'algorithm' for mid and max appears to be just adding 1.5 and 2.25 > to the threshold. I wasn't aware of this, or understand why (other than > the need to set it to something!), so if you have an alternative, I'd > like to hear. > > Also attached are mri2.c and sig.c, which contains the core fdr2vwth > routine. It appears that "if no values meet the FDR criterion, then a > value slightly smaller than the smallest p is returned." > > I've updated the code to print to the terminal the number of vertices > having a P < the fdr min, although it seems to always be a large number > of vertices because the fdr min is a positive value, and a typical > result has both positive and negative P values. > > Nick > > > > On Thu, 2008-12-11 at 17:09 -0600, Michael Harms wrote: > > Hello, > > I'm curious, what algorithm is used for setting the "mid" and "max" > > threshold values in QDEC when using the "Set Using FDR" button? > > > > And, what does the algorithm do for setting the "min" threshold when no > > single p-value is significant enough to satisfy the necessary inequality > > for the specified FDR Rate? > > In that case, is the resulting "min" just set to the -log10(p) of the > > most significant p-value? > > > > If easy to implement, it would be handy if the output to the terminal > > reported the number of vertices with P < than the FDR determined "min" > > threshold. > > > > cheers, > > Mike H. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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