Dear Kim, That's right, T=Inf is the correct threshold. I.e., there is *no* threshold that will control FDR at 5%. This might help: load xSPM Ps=xSPM.Ps; S=xSPM.S; P_FDR = spm_P_FDR(spm_invNcdf(1-Ps(1)),[1 Inf],'Z',1,Ps') subplot(2,1,1) plot((1:S)/S,Ps,'-o',(1:S)/S,(1:S)/S*P_FDR);xlim([0 0.5]);ylim([0 0.05]) title('Observed P versus Expected') subplot(2,1,2) loglog((1:S)/S,Ps,'-o',(1:S)/S,(1:S)/S*P_FDR);xlim([0 0.5]);ylim([0 0.05]) title('Observed P versus Expected, log-log') As you'll see, P_FDR is 0.1789. If you ask for FDR control at 0.2, you should see some voxels. -Tom On Thu, Jul 21, 2011 at 12:38 PM, Guillaume Flandin < [log in to unmask]> wrote: > Dear Kim, > > I cannot see anything wrong, you seem to be in the situation where there > is no signal in your data and the BH procedure, as implemented in SPM, > returns Inf in this case. > > spm_uc_FDR(0.05,xSPM.df,xSPM.STAT,xSPM.n,xSPM.Ps') > > See slide 43 of this talk: > http://www.fil.ion.ucl.ac.uk/spm/course/slides11/06_RFT_etc_FIL2011May.ppt > > You can also compute: > spm_invTcdf(1-0.05/33012,24) = 6.0479 > which is the 0.05 critical threshold, that your data do not reach. > > I copy this email to Tom Nichols who might be able to tell us more. > > Best regards, > Guillaume. > > > On 21/07/11 11:55, Veroude, K. wrote: > > Dear Guillaume, > > > > Yes I changed topoFDR to 0 in SPM_defaults. Attached you can find the > xSPM.mat. > > > > Thanks, > > > > Kim > > > > ________________________________________ > > Van: Guillaume Flandin [[log in to unmask]] > > Verzonden: donderdag 21 juli 2011 12:12 > > Aan: Veroude, K. > > Onderwerp: Re: [SPM] FDRp: Inf in SPM 8 > > > > Dear Kim, > > > > so I assume that you are using voxel-wise FDR (ie you switched the > > topoFDR option to false)? > > When you are looking at this result, there should be a variable called > > 'xSPM' in the MATLAB workspace, could you send it to me? > >>> save xSPM.mat xSPM > > > > Many thanks, > > Guillaume. > > > > > > On 21/07/11 08:32, Veroude, K. wrote: > >> Dear Guillaume, > >> > >> This is the Results window we get when applying FDR correction at p < > 0.05. Any help would be appreciated. > >> > >> Best wishes, > >> > >> Kim > >> > >> > >> -----Oorspronkelijk bericht----- > >> Van: Guillaume Flandin [mailto:[log in to unmask]] > >> Verzonden: woensdag 20 juli 2011 16:27 > >> Aan: Veroude, K. > >> Onderwerp: Re: [SPM] FDRp: Inf in SPM 8 > >> > >> Dear Kim, > >> > >> can you give me more details on what you are observing? A screenshot of > >> the Results Graphics window would be useful to start with. > >> > >> Best regards, > >> Guillaume. > >> > >> > >> On 20/07/11 09:40, Kim Veroude wrote: > >>> Hi, > >>> > >>> We have a similar problem, when applying FDR correction in SPM8 it > >>> shows T = Inf. Have you found a solution for this? > >>> > >>> Thanks! > >>> > >>> Kim > >>> > >>> > >> > >> > > > > > > -- > > Guillaume Flandin, PhD > > Wellcome Trust Centre for Neuroimaging > > University College London > > 12 Queen Square > > London WC1N 3BG > > > -- > Guillaume Flandin, PhD > Wellcome Trust Centre for Neuroimaging > University College London > 12 Queen Square > London WC1N 3BG > -- __________________________________________________________ Thomas Nichols, PhD Principal Research Fellow, Head of Neuroimaging Statistics Department of Statistics & Warwick Manufacturing Group University of Warwick, Coventry CV4 7AL, United Kingdom Web: http://go.warwick.ac.uk/tenichols Email: [log in to unmask] Phone, Stats: +44 24761 51086, WMG: +44 24761 50752 Fax: +44 24 7652 4532 Now out! *Handbook of fMRI Data Analysis*, by RA Poldrack, JA Mumford & TE Nichols http://go.warwick.ac.uk/tenichols/publications/books -- __________________________________________________________ Thomas Nichols, PhD Principal Research Fellow, Head of Neuroimaging Statistics Department of Statistics & Warwick Manufacturing Group University of Warwick, Coventry CV4 7AL, United Kingdom Web: http://go.warwick.ac.uk/tenichols Email: [log in to unmask] Phone, Stats: +44 24761 51086, WMG: +44 24761 50752 Fax: +44 24 7652 4532 Now out! *Handbook of fMRI Data Analysis*, by RA Poldrack, JA Mumford & TE Nichols http://go.warwick.ac.uk/tenichols/publications/books