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Carlos, The problem points are the super-high intensity points in the RPV image. Those super-rough regions are artificially shrinking your FWHM estimate which is sending your RESEL count through the roof (can you report what your FWHM & Resel counts are?) The solution is to mask out (better yet, understand what's going on with) those super-rough voxels. Worst case, take the mask image created by SPM, and then mask out the voxels with super-high RPV values (with some ImCalc arithmatic) and create a new mask that you can uses as an 'explicit mask' in a new analysis. Hope this helps! -Tom On Wed, Oct 8, 2008 at 8:43 PM, Carlos Faraco <[log in to unmask]> wrote: > On Mon, 6 Oct 2008 21:51:26 +0100, Thomas Nichols <[log in to unmask]> > wrote: > > > > > >Are the problems related to smoothness estimation? > > Do you mean at the individual level or 2nd level? How can I see values for > this? > > >I.e. is the smoothness FWHM or Resels NaN as well? Or, are their strange > values for the > >"Expected voxels per cluster" or "Expected number of clusters"? Is the > number of the > >voxels in the analysis what you expect? (Mask not way too large or too > >small?) > > On the within group data I receive the following output: > > For Stroop task, using default values on results: > 1. Using no correction: some clusters, Expected voxels per cluster (EVC) = > .003, Expected # of clusters (E#C) = 64075.98, Expected FDR = .66 > 2. Using FDR: No suprathreshold clusters, EVC = NaN, E#C = NaN, EFDR = .66 > 3. Using FWE: 2 clusters, 1 large one with 199336 voxels, EVC = 221, E#C = > .05, FDR = .90 > > For OSPAN task: > 1. No correction: Showed scattered, random looking activation and gave the > following warning many times > Warning: Returning NaN for out of range arguments > > In spm_Pcdf at 88 > In spm_P_RF at 106 > In spm_P at 48 > In spm_list at 487 > > I pressed Ctrl+C to stop the repition of these warnings and the volume > table > had a 25 page list of clusters all with NaNs for Pcorrected. > > 2.Using FDR: same as in Stroop, except EFDR = .10 > > 3. Using FWE: no clusters, EVC=0.000, E#C = 393619779.31, EFDR=.10 > > The # of voxels for the analyses were around 205,000 voxels. > > >If there are NaN's in the smoothness estimate, look at the FWHM image > >(compute from the RPV image with ImCalc as FWHM = RPV.^(1/3)). Viewing > this > >image with CheckReg with other images (e.g. the mask, or T image, ResMS > (or > >its square root), etc). If the is *really* irregularly shaped (i.e. no > >contiguous voxels) it is possible to have almost all NaN's in the RPV > image. > > The RPV images for the group data have some NaN values outside of the > brain, > which as you suggested may be normal. However, the images are of a very low > intensity, from about .002 - 3.0, expect for a few high intensity points. > The FWHM from this doesn't show much of course. > > I hope this helps to describe the problem. Also, some of the activation on > the single subject data looks really bad, just big huge blobs. > > Thanks, > > Carlos > > > >-Tom > > > > > >On Mon, Oct 6, 2008 at 9:08 PM, Carlos Faraco <[log in to unmask]> wrote: > > > >> Dear SPMers, > >> > >> Today I read through many of the posts regarding NaNs, however I am > still > >> confused as to what would be the best remedy for my situation. > >> > >> The problem is I keep on receiving NaNs for the p-vals on the second > level > >> analysis. I tried changing the NaNs to 0s in the con images (which seem > to > >> appear only or mostly outside the brain; and becasue I read not to do > this > >> for the beta images) using ImCalc but that still doesn't work. I > therefore > >> checked some files from some other studies we had previously done, and > it > >> appears that setting voxels outside the brain to NaN is normal SPM > >> behavior. > >> > >> Is the fix for this then something that has to be modified within the > SPM > >> code? > >> > >> Thanks, > >> > >> Carlos Faraco > >> > >> > > > > > >-- > >____________________________________________ > >Thomas Nichols, PhD > >Director, Modelling & Genetics > >GlaxoSmithKline Clinical Imaging Centre > > > >Senior Research Fellow > >Oxford University FMRIB Centre > > > > > > -- ____________________________________________ Thomas Nichols, PhD Director, Modelling & Genetics GlaxoSmithKline Clinical Imaging Centre Senior Research Fellow Oxford University FMRIB Centre