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Dear Nelleke, Unless your ROI consists of a single voxel, I won't use an uncorrected test. When the search region is very small, a cluster test can not work so well (even if you us a high threshold, it's likely that a cluster will touch an edge, which the theory doesn't account for very well). Hence for small ROI search regions, I'd recommend using corrected *voxel* wise inferences. -Tom On Fri, Jul 4, 2008 at 2:26 PM, Wouwe, Nelleke van <[log in to unmask]> wrote: > Hi Tom, > > Thanks for the reference and explanation. Would you also recommend, since I > am performing a ROI analysis, doing an uncorrected test, at P=0.05 or 0.01 > for the regions I am interested in? > > regards > Nelleke > > ________________________________ > > From: FSL - FMRIB's Software Library on behalf of Thomas Nichols > Sent: Fri 7/4/2008 7:43 AM > To: [log in to unmask] > Subject: Re: [FSL] thresholding question > > > Hi folks, > > Saad's right, as the threshold drop's the expected EC becomes a worse > approximation of the expected number of clusters. There's yet another > problem, though: For high thresholds, the null distribution of cluster size > is approximately exponential. As the threshold drops this approximation > gets worse, and cluster P-values get less accurate. > > For examination of RFT cluster size performance as a function of threshold > and smoothness, see: S. Hayasaka and T.E. Nichols. Validating cluster size > inference: random field and permutation methods. NeuroImage, 20:2343-2356, > 2003. > > > On Thu, Jul 3, 2008 at 2:22 PM, Saad Jbabdi <[log in to unmask]> wrote: > > > My -little- understanding of GRF is that: > > The rationale behind GRF is that the -expected- euler characteristic > (EC) approximates the FWE probability. > EC basically counts the number of peaks minus the number of holes > (after thresholding). If your threshold is too low, you will have many > holes, and the EC will not represent the number of peaks, which you want in > order to approximate the FWE.. > > Saad. > > > On 3 Jul 2008, at 13:52, Wouwe, Nelleke van wrote: > > > Hi Tim, > > I am not sure if I understand you correctly: are you saying > that I > cannot use Z-values below 2 because GRF theory is not valid > anymore? Why > is that? > > Thanks for your help > Nelleke > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto: > [log in to unmask]] On > Behalf Of Tim Behrens > Sent: 03 July 2008 14:20 > To: [log in to unmask] > Subject: Re: [FSL] thresholding question > > Hi - if you are using Gaussian Random Field theory for your > inference > (i.e. if you are using Flame and not randomise) then it > breaks down at > low Z values (less than about 2). > > Cheers > > T > > On 3 Jul 2008, at 12:56, Nelleke Van Wouwe wrote: > > > Hi all, > > From some previous discussions and Matt Brett's page > on cluster > thresholding I understand that you chose the z value > based on the > activation you are looking for;high z for small > regions and low Z for > big regions (given p<0.05, corrected). > > I performed a ROI analysis (pre-masked the data with > part of the > fusiform gyrus and parahippocampal gyrus)with a > (corrected) cluster > significance threshold of P=0.05 and I tried a very > low Z threshold of > > > 1.1. > According to the clusterlist below I find a large > cluster (232 > voxels) that > is significantly active (P<0.05) with z-max 1.9. > > I wonder if there are any rules of thumb to > determine an appropriate Z > > > threshold (other than the default) and would this z > = 1.1 still be a > reasonable threshold? > > Thanks! > Nelleke > > Cluster List > Cluster Index Voxels P -log10(P) Z-MAX Z-MAX X (mm) > Z-MAX Y (mm) Z- > MAX Z > (mm) Z-COG X (mm) Z-COG Y (mm) Z-COG Z (mm) COPE-MAX > COPE-MAX X > (mm) COPE- > MAX Y (mm) COPE-MAX Z (mm) COPE-MEAN > 5 232 0.0356 1.45 1.83 42 -50 -22 42.7 -47.8 -24.2 > 193 42 -42 -30 149 > 4 41 0.039 1.41 2.26 -44 -62 -26 -42.7 -60.2 -25 243 > -44 -62 -26 163 > 3 26 0.0394 1.4 1.68 34 -34 -20 31.5 -35 -19 134 34 > -34 -20 107 > 2 24 0.0394 1.4 1.45 -32 -38 -20 -30.8 -38.3 -18.6 > 103 -32 -38 -20 > 87.6 > 1 1 0.0405 1.39 1.15 24 -48 -6 24 -48 -6 110 24 -48 > -6 110 > > > > > ********************************************************************** > This email and any files transmitted with it are > confidential and > intended solely for the use of the individual or entity to > whom they > are addressed. If you have received this email in error > please notify > the system manager. > > ********************************************************************** > > > > > > --------------------------------------------------------------------------- > Saad Jbabdi, > Postdoctoral Research Assistant, > Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222545 (fax 222717) > [log in to unmask] http://www.fmrib.ox.ac.uk/~saad<http://www.fmrib.ox.ac.uk/%7Esaad> > > --------------------------------------------------------------------------- > > > > > > > > > -- > ____________________________________________ > 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