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 >> > _______________________________________________ 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.
