Is there an updated version of mri_mcsim available? When I try to run it, all I get back are error messages that none of the option flags are valid (e.g., ERROR: Option --base unknown).
Thanks, Jim Jim Porter, M.A. Graduate Student Clinical Science& Psychopathology Research University of Minnesota On 7/22/64 1:59 PM, James Porter wrote: > Hello Doug- > > When using mri_mcsim, is there an option to reduce the iterations of > fwhm values? I'd like to create a database of sims within an in-house > average subject as well as within different labels, but I have no need > for 30 fwhm values. If I could restrict it to just a few choice > values, that would be great. > > Jim Porter, M.A. > Graduate Student > Clinical Science& Psychopathology Research > University of Minnesota > > > On 7/22/64 1:59 PM, Douglas N Greve wrote: >> use the value in the fwhm.dat. I would always round up to be safe. >> >> doug >> >> Michael Waskom wrote: >>> Hi Doug, >>> >>> This looks very helpful! Should we use the fwhm size corresponding >>> to the argument of the --fwhm flag when recon-all runs mri_surf2surf >>> (for anatomical stats), or round the measure found in the fwhm.dat >>> of the glmfit dir? >>> >>> Thanks, >>> Mike >>> >>> ---------- Forwarded message ---------- >>> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>> >>> To: port...@umn.edu <mailto:port...@umn.edu> >>> Date: Tue, 27 Apr 2010 11:17:24 -0400 >>> Subject: Re: [Freesurfer] question about clustering simulation >>> Yea, that was a bug in the simulation program I used. I did confirm >>> that the simulations were done on the correct hemisphere. Feel free >>> to edit the files. I'll fix the master when I get a chance. >>> >>> doug >>> >>> James Porter wrote: >>> >>> Doug- >>> >>> Let me be the first to say thank you for saving me massive amounts >>> of simulation time. One bug though: the right hemisphere files say >>> they were created using the left hemisphere, and mri_surfcluster >>> rejects them. Would it be verboten to just alter the csd files, or >>> do you have versions that were created off of fsaverage's right >>> hemisphere? >>> >>> matacao:mult-comp-cor porterj$ head >>> fsaverage/rh/cortex/fwhm19/abs/th33/mc-z.csd >>> # simtype null-z >>> # anattype surface fsaverage lh >>> # FixGroupSubjectArea 1 >>> # merged 0 >>> # contrast NA >>> # seed 1271355821 >>> # thresh 3.300000 >>> # threshsign 0.000000 >>> # searchspace 74490.928733 >>> # nullfwhm 19.000000 >>> >>> Jim Porter, M.A. >>> Graduate Student >>> Clinical Science& Psychopathology Research >>> University of Minnesota >>> >>> >>> On 7/22/64 1:59 PM, Douglas N Greve wrote: >>> >>> 1. Correct on both counts. When I wrote the simulation, I was >>> only trying to replicate the random fields analysis. But with >>> a simulation, you have more freedom that I am not yet >>> exploiting. >>> 2. This is what we are already doing with mc-z >>> 3. I'm working on this as well. It turns out that the random >>> fields approximation works a lot better when using the number >>> of vertices. >>> >>> Also, I've run mc-z simulations under a bunch of thresholding >>> and FWHM conditions for whole-hemisphere cortex labels. These >>> will be integrated in new version of FS, but I've put them >>> here >>> >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mult-comp-cor.tar.gz >>> >>> >>> as well. There's a README file in there. This will make >>> running your own time-consuming simulations unnecessary (when >>> using the cortex mask at least). >>> >>> doug >>> >>> Anthony Dick wrote: >>> >>> Hello all, >>> >>> I am interested in using the mri_glmfit simulation to >>> control for multiple comparisons in data I have run on the >>> surface in AFNI. Before doing this, I have a few questions: >>> >>> 1. What does the simulation with the mc-z flag do, >>> exactly? It claims to be comparable to AFNI's AlphaSim, >>> but it takes a maximum cluster area for each iteration, >>> which is not exactly what AlphaSim does. Here is my guess: >>> >>> Given a surface, a given smoothness of the data, and a >>> given per-vertex threshold, for each iteration the >>> simulation populates that surface with random data taken >>> from a normal distribution, thresholds the data, and >>> applies the smoothness of the actual data (supplied as an >>> input parameter). It then computes the maximum cluster >>> size in area for that "image". Doing this n iterations >>> gives a distribution of maximum cluster sizes that occur >>> for random data of a given smoothness, and taking cluster >>> sizes above a certain percentile rank controls for the FWE >>> at a level equal to that percentile rank (e.g., 95th% >>> controls for FWE = .05). AlphaSim does something similar, >>> although instead of taking maximum cluster sizes at each >>> iteration it computes all given cluster sizes. AlphaSim >>> also allows for different cluster connectivity radius, but >>> it seems Freesurfer computes only for neighboring >>> vertices. All in all, if this is correct, it seems like a >>> good implementation. >>> >>> 2. It is my understanding that one could bypass running >>> the glm in Freesurfer and only compute the simulation, as >>> the simulation only needs information about the surface, >>> and the smoothness of the data (which are supplied by the >>> user). To do so, you have to "fake out" Freesurfer to >>> bypass glm, but that turns out to be pretty painless. >>> >>> 3. In a future distribution, is it possible to modify this >>> procedure to also output maximum cluster sizes in terms of >>> number of nodes, rather than area? >>> >>> Can you please let me know if I am mistaken in any of >>> these assumptions? Thanks in advance. >>> >>> Anthony >>> >>> >>> >>> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>> Phone Number: 617-724-2358 Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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