Can you send your mri_glmfit and mri_surfcluster command-lines? doug
James Porter wrote: > Sorry, I mistyped. To clarify, the original qdec analyses were run on > the 10mm smoothed data from qcache, and the sims were then run with > and without passing the value from fwhm.dat into the FWHM flag in > mri_glmfit. > > --------- > Jim Porter > Graduate Student > Clinical Science & Psychopathology Research > University of Minnesota > > James Porter wrote: >> I have recently run simulations with and without the FWHM flag, and >> the results were 100% identical, in both the mgh output and cluster >> summary files. From what is below, I would think that the results >> should have changed in at least some way. The original qdec analysis >> was run with 10mm smoothing, and the sims (mc-full, 10k) were run >> with and without 10mm smoothing. >> >> Is there a certain point at which one would not expect smoothing in >> the simulations to not matter? >> >> --------- >> Jim Porter >> Graduate Student >> Clinical Science & Psychopathology Research >> University of Minnesota >> >> Douglas N Greve wrote: >>> <div class="moz-text-flowed" style="font-family: -moz-fixed">1) The >>> smoother the data, the more likely a cluster will be found by >>> chance. When the data are created, they start with some smoothness >>> level. When you smooth them you add more. So you need to match the >>> total level of smoothing when you do the simulations, otherwise your >>> clusters will be way too significant. mri_glmfit creates a fwhm.dat >>> file with an estimate of the total smoothness. >>> >>> 2) Just if they are nearest neighbors. There is no option to tinker >>> with this. >>> >>> 3) Vertices in the maps created by the simulation are thresholded at >>> the level you pass. This is what defines the cluster. >>> >>> doug >>> >>> Dankner, Nathan (NIH/NIMH) [F] wrote: >>>> Hello all, >>>> >>>> I have a couple of questions regarding the way the cluster >>>> correction simulation in freesurfer works. I've read the wiki >>>> pages on the subject, but if I've missed something and any of this >>>> is answered elsewhere please let me know. My technical knowledge >>>> of these things is not great so I am just trying to get some >>>> background. First of all, how does smoothing the data prior to >>>> running the simulation affect the results? I've run corrections on >>>> the same data smoothed with a 10mm FWHM, and also on completely >>>> unsmoothed data, and the cluster results were different. Secondly, >>>> what determines whether vertices are neighbors or not? Is there an >>>> option to tinker with this or is it predetermined? Lastly, how do >>>> the p values of individual vertices factor into the simulation? >>>> Are they taken into account when the determination of the max >>>> cluster size under the null hypothesis is performed? Thanks in >>>> advance, >>>> >>>> Nate >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> [email protected] >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
