On 07/08/2016 02:21 PM, Arkadiy Maksimovskiy wrote: > Hello, > > I apologize if the questions are trivial- I have checked the archives, > but could not find anything on this. > > I have run a t-test between two groups on cortical thickness, and used > mri_glmfit-sim for pos, neg, and abs versions. > > 1. If my FSGD is organized as: > Group 1 > Group 2 > > and my matrix file is 1 -1 > > Would a blue result in an absolute version indicate that Group 1 < > Group 2? Blue would mean that Group 1 < Group 2 > > 2. When running the command: "less" on > "cache.th13.pos.sig.cluster.mgh", I am getting 1 significant cluster, > however, when running the same command on the "absolute" version of > this file, there is nothing significant. Do you know why this might be > the case? A signed test (eg, pos or neg) has a different voxel-wise threshold than an unsigned test (eg, abs). By default, FS computes statistics in an unsigned manner, so when you specify a cluster-forming threshold with abs, that is the actual threshold that is used. When you use pos or neg, the cluster-forming threshold is made more liberal to account for the fact that you are doing a signed test. For a cluster that is all negative, using neg will result in a more liberal threshold and so a larger cluster which may be more significant. > > Much appreciated, > > Arkadiy > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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