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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
