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Hi Yang Hu, Yes, that's right. The only thing I'd change in your description is that TFCE is a voxel-based type of *statistic* (i.e., not really a correction method; it still requires correction after it has been computed). All the best, Anderson On Mon, 25 Feb 2019 at 20:27, huyang <[log in to unmask]> wrote: > Hi, Anderson > > Thank you so much for very detailed and easy-to-read explanation.One > further question is the popular TFCE method, which seems to make a > transformation of raw statistic map by incorporating both its height (how > high the statistic of a voxel is) and extent (Is this voxel in a cluster) > information. The transformed maps (i.e., TFCE maps) go through a > permutation test to obtain corrected p-values. Therefore, TFCE method is a > voxel-based (instead of cluster-based) correction method but considering > the spatial cluster information, in comparison with the original > voxel-based method. Is my understanding right? Thanks! > > Best, > > Yang Hu > > 在 2019-02-25 20:19:42，"Anderson M. Winkler" <[log in to unmask]> 写道： > > Hi Yang Hu, > > Please see below: > > On Sun, 24 Feb 2019 at 05:01, huyang <[log in to unmask]> wrote: > >> Dear FSL experts and users, >> >> (1) Suppose that I collected two groups of data and computed the >> voxel-wise metrics (for instance, gray matter volume). I would like to test >> the hypothesis that whether the two groups differ in some brain regions. I >> could get a voxel-wise P-value map by conducting a Two-sample T-test in >> each voxel independently or by conducting a permuation test in each voxel >> independently. This is the difference between parametric and non-parametric >> hypothesis testing, I think. >> > > In both cases you'd do a two-sample t-test. In the parametric you'd use a > formula that is based on some assumptions or knowledge about the data to > obtain p-values. In the permutation case, you'd shuffle the group > membership so as to obtain a permutation-based p-value. > > >> My question is that when using FSL's *randomise*, permutation test is >> used for calculating raw P-values? >> > > Yes. > > >> >> (2) After I get a voxel-wise P-value (T-statistic) map, I need to correct >> these P-values for multiple comparisons. >> > > One way to see this is, as you say, need to correct the p-values. Another > way to see this is that you need to obtain p-values that take into account > the multiplicity of the tests, even if the uncorrected p-values had not > even been computed. For both RFT and permutation testing, one does not, in > fact, need to ever compute the uncorrected, "raw" p-values, and it's > possible to proceed straight to the FWER-adjusted p-values. > > >> Random field theory could be used to estimate the P-value threshold at a >> FWER of 0.05 (voxel-based) or cluster size threshold at a FWER of 0.05 >> (cluster-based). >> > > Yes. Note that cluster-level statistics are not a form of correction. > Rather, they are statistics on their own right, for which both uncorrected > and corrected p-values can be computed (it turns out that, for cluster, > uncorrected p-values seldom make any sense, because clusters move around, > so we always think about corrected p-values in that case). > > >> FSL's *randomise* could also be used for voxel-based/cluster-based >> thresholding. My question is that how could permutation be used for >> multiple comparison correction? Is it based on the maximal statistic (the >> maximum of a statistic map) distribution during the permutations? >> > > Yes. For the test statistic obtained at each voxel, the FWER p-value is > computed by considering the distribution of the maximum statistic across > the image. > > All the best, > > Anderson > > > >> >> I read the related papers but these are too technical (difficult) for me, >> and I would like to have a basic but not-too-wrong conception. Many thanks. >> >> Best, >> >> Yang Hu >> >> >> >> >> ------------------------------ >> >> To unsubscribe from the FSL list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >> > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > > > > > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1