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Hi, Thank you very much for this detailed explanation. I am looking forward to seeing TFCE option in FEAT. Cheers, Auer, Tibor M.D. Biomedizinische NMR Forschungs GmbH am Max-Planck Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Germany Phone/Work: +49-(0)551-201-1725 Phone/Home: +49-(0)551-250-4576 Mobile: +49-(0)176-8012-7921 Mail: [log in to unmask] -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Steve Smith Sent: Monday, March 02, 2009 12:10 PM To: [log in to unmask] Subject: Re: [FSL] TFCE in fMRI Hi - the TFCE option in fslmaths is there in case you are interested in the TFCE enhancement (e.g.) to a raw zstat image - to enhance cluster-like aspects of the data. However, as Reza said, it is not able to convert TFCE-enhanced values into p-values, because there is not currently a simple direct conversion - currently, the only way to convert TFCE scores into p-values is via randomise. You can't apply randomise to FMRI first-level timeseries analysis because of the temporal smoothness in the data - you could maybe whiten the data and then run randomise (a la Bullmore) but we've not tested that. You can apply randomise to higher-level analyses (see previous posts) - in general this is usable for most if not all second- level designs, though currently only allows OLS modelling, i.e. doesn't apply the more advanced variance modelling that FLAME does. Cheers. On 2 Mar 2009, at 10:48, Auer, Tibor MD. wrote: > Hi Reza, > > Thank you for your fast reply. > > It was my fault. On the page (http://www.fmrib.ox.co.uk/fsl/randomize/index.html > ) I have read that fslmaths can be used to test TFCE "on an > existing stats image". But it seems it is true just after applying > randomise. Is it correct? Or what else "fslmaths -tfce" is for? > > Another questions. According to the page mentioned above "randomise" > is an option for simple GLM (t-tests, one-way ANOVA, simple > correlation). In fMRI it means some cases of higher level analysis. > What about 2-way ANOVAs? What about 1st level, where design matrix > contains canonical HRF? And when we use nuisance effects (e.g. > motion-correction parameters, or temporal derivative of HRF), the > exchangeability of data is not assured. Does it means that randomise > is not advised to use in these cases? > > Best, > > Auer, Tibor M.D. > Biomedizinische NMR Forschungs GmbH > am Max-Planck Institut für Biophysikalische Chemie > Am Fassberg 11 > 37077 Göttingen > Germany > Phone/Work: +49-(0)551-201-1725 > Phone/Home: +49-(0)551-250-4576 > Mobile: +49-(0)176-8012-7921 > Mail: [log in to unmask] > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On > Behalf Of Reza Salimi > Sent: Monday, March 02, 2009 11:01 AM > To: [log in to unmask] > Subject: Re: [FSL] TFCE in fMRI > > Hi Tibur, > applying the TFCE to a statistical map (i.e., a t- or z-stat map) > cannot be directly used for a statistical inference (i.e., > thresholding to find activation blobs in the brain), > and since there is no parametric form for the TFCE statistic, you > need to run a nonparametric (randomise) analysis, with TFCE > inference and threshold the output p-value volume (which is > *tfce*corrp* volume in randomise). > cheers > > > > > 2009/3/2 Auer, Tibor MD. <[log in to unmask]> > Dear FSL Users, > > I try to use TFCE (Threshold Free Cluster Enhancement) in fMRI. I > have read that "fslmath" can apply TFCE on a previously calculated > statistical map (e.g. ztats1.nii.gz). > > To make everything easier, I have written a script to produce > activation map after TFCE (see attached). > I used the pre-fixed options 2 0.5, and according to my > understanding thresholded the resulted image with 0.95 to get p=0.05 > equivalent. The rest of the script is just to overlay and produce > image. > > The attached script produces more sensitive however quite noisy image. > I ask someone with more knowledge on TFCE to check whether my > implementation is correct. > > Thanks, > > Auer, Tibor M.D. > > Biomedizinische NMR Forschungs GmbH > > am Max-Planck Institut für Biophysikalische Chemie > > Am Fassberg 11 > > 37077 Göttingen > > Germany > > Phone/Work: +49-(0)551-201-1725 > > Phone/Home: +49-(0)551-250-4576 > > Mobile: +49-(0)176-8012-7921 > > Mail: [log in to unmask] > > > > > > > > > -- > G. Salimi-Khorshidi, > D.Phil. Student, Dept. of Clinical Neurology, University of Oxford. > [log in to unmask] http://www.fmrib.ox.ac.uk/~reza > FMRIB Centre, John Radcliffe Hospital, > Headington, Oxford, OX3 9DU > Tel: +44 (0) 1865 222466 Fax: +44 (0)1865 222717 > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------