Hi John, mri_glmfit-sim actually runs on the GLM dir created when you run mri_glmfit (it does not take a separate directory). It applies the correction to all the contrasts in the GLM dir, so you just need to set up a GLM with the contrast you want to correct.
doug John Richey wrote: > Dear freesurfer experts, > > I have a question about the conceptual use of mri_glmfit-sim. I wish to > apply permutation based cluster-correction to my between-groups results > (patients vs controls), and it is not clear to me which volume should be > the input for this type of simulation. > > For example, the acceptable input for mri_glmfit-sim appears to be only the > ".ces" map, which is not present in my between-groups directory, but only in > my lower-level one-sample group means (osgm). This raises the question of > whether to run the permutation algorithm 1) one time on the .ces map that > results from the total sample OSGM (i.e. patients + controls), or 2) > separately on OSGM for patients and then controls. Probably I am mistaken > but neither seem to be conceptually correct, as I am mainly interested in > the cwp for clusters emerging in the between-groups contrast. > > Any help would be greatly appreciated! > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- 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.
