5000 permutations is the generally recommended minimum, while 10000 is even better. See the FSL page on randomise http://www.fmrib.ox.ac.uk/fsl/randomise/index.html for the confidence limits for a nominal alpha of 0.05 as a function of the number of permutations.
Also, I don't know how complicated your statistical model is, but I'm not sure how the permutation engine within mri_glmfit implements its permutation testing in the case of complicated models involving covariates. It is a non-trivial issue. See the above FSL page, and the references cited therein, for a discussion of some of the technical issues involved when performing permutation testing in the presence of covariates. cheers, -MH On Mon, 2010-10-11 at 12:10 +0800, Jay Ives wrote: > Hi Micheal, > > Thanks. Looks like I will have to dump all my results done with mc-z! > > Unfortunately the Freesurfer Wiki is mute on the use of permutation, > unless there is some tutorial I haven't found. > How many permutations should one run? > Any other helpful hints? > > Cheers.......J > > On Mon Oct 11 9:05 , "Michael Harms" sent: > > > Hi Jay, > Permutation testing will give the most accurate results. > > cheers, > -MH > > > Hi Experts, > > > > Which option is best to use: mc-z or perm? > > I have read that perm gives more accurate results than mc-z, > as it uses > > the actual data rather than fake data to estimate the null > distribution. > > When I use perm, I get no significant clusters. > > When I use mc-z, almost all clusters are significant. > > > > Thanks......J_______________________________________________ > > 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. > > > > _______________________________________________ > 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
