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On Sat, Sep 11, 2010 at 7:03 PM, Xu Chen <[log in to unmask]> wrote: > Thanks for your explanation, Reza! That helps. I missed the nonparametric > part. I am working on the cluster-wise inference using "randomise". > > that is a nonparametric inference, however, if you take ONLY the T-stat image from randomise and do some-analysis-on-your-own, then you cannot say "using randomise". > But seems to me , the threshold selection (the parameter after -c ) for the > clusters seems a little bit "random". Do you have any recommendations on the > strategy of the threshold selection? > > By random you mean arbitrary :) This is the reason why TFCE is introduced to the field. In general, 3'ish (±.5) on your T-stat should be a safe threshold (though it's hard to say a single value for EVERY study). > Thanks > > Jerry > > > On Sat, Sep 11, 2010 at 5:41 AM, Reza Salimi <[log in to unmask]> wrote: > >> Jerry, >> >> On Sat, Sep 11, 2010 at 12:06 AM, Xu Chen <[log in to unmask]> wrote: >> >>> Hi, FSLers >>> >>> Just curious how the uncorrected p in TFCE get calculated? I >>> thought that the uncorrected-p was simply computed based on the t stat >>> value (in the file of *_tfce_tstat) with the consideration of the DOF. But I >>> just noticed the inconsistency between the one I calculated based on the >>> tstat and the one in the Uncorrected P file (*_tfce_p_tstat). Seems I >>> missed something there. >>> >>> randomise is a nonparametric inference, hence, no T-test with a DOF takes >> place here. >> Anyway, as you said, we advocate the use of corrected P-value, however, >> there is an uncorrected P-value image in the result folder. >> The uncorrected P-values are purely voxel-wise; calculated for each voxel >> using its individual distribution. >> >> >>> I understand that ideally, the Corrected-P in TFCE should be used. >>> However, if the resultant image in Corrected-P doesn't show any significant >>> activations at a certain threshold (e.g. p=0.95) , which one should be used >>> to report the result, the tstat value (_tfce_tstat) or the Uncorrected -P >>> (_tfce_p_tstat)? >>> >> >> In order to have the most reliable, i.e., statistically powerful >> inference, you better use a family-wise error measure, which is why >> corrected P-values of the TFCE are recommended. >> Using the T-stat, you can only perform a voxel-wise parametric inference, >> which is shown to be less sensitive than cluster and TFCE. >> And for the uncorrected TFCE P-values, you will have a result that is not >> corrected for multiple comparison, which makes it questionable. >> >> hope it helps ... >> >> >>> >>> Thanks >>> >>> Jerry >>> >> >> >> >> -- >> Reza Salimi-Khorshidi, >> DPhil Candidate, FMRIB Centre of the University of Oxford (Linacre >> College) >> Associate Member, Oxford-Man Institute for Quantitative Finance, >> University of Oxford >> >> Email: [log in to unmask]; Tel: +44 (0) 1865 222704; Fax: +44 (0)1865 >> 222717 >> Address: FMRIB Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK >> >> >> > -- Reza Salimi-Khorshidi, DPhil Candidate, FMRIB Centre of the University of Oxford (Linacre College) Associate Member, Oxford-Man Institute for Quantitative Finance, University of Oxford Email: [log in to unmask]; Tel: +44 (0) 1865 222704; Fax: +44 (0)1865 222717 Address: FMRIB Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK