That command would be for an mc-z simlation, not a permutation. But you are right the perm does not allow non-orthogonal matrices. The mc-z synthesizes a z-field, smooths it, thresholds it, and extracts clusters, repeats this 10000 times to get an idea of what cluster sizes should be expected under the null. Permutation randomly changes the rows of the design matrix, runs the analysis, gets a z-map, thresholds it, and extracts clusters, repeats this 10000 times to get an idea of what cluster sizes should be expected under the permutation null.
doug Rafa x wrote: > Dear Doug I’ve tried runnig the command: > > mri_glmfit-sim --glmdir lh.fsgd_subj_gauss001 --sim mc-z 625 2.3013 > mc-z.pos.3 --sim-sign pos > > And the following error appears: > "ERROR: desig matrix is not orthogonal, cannot be used with permutation." > > As I’ve search in the forum list, I have found that the --sim perm > option does not work with continuous variables, but that --sim mc-z > does, which are the differences between this two methods? > > Bests, > Rafa. > > > 2011/1/26 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > >> For the permutation sim, the fwhm should be set to 0. Why are you not using >> mri_glmfit-sim? I would strongly recommend it as that will make sure that >> all the arguments are correct. >> >> doug >> >> Rafa x wrote: >> >>> Dear Freesurfers, >>> In Freesurfer v5.0 when I try to run the command: >>> >>> mri_glmfit --surf CNTRL_MCI_RAFA_average lh --C contrast.mat --fsgd >>> fsgd.txt dods --mask lh.fsgd_subj/mask.mgh --y >>> CNTRL_MCI_RAFA_stats/lh.fsgd_subj.mgh --sim perm 625 2.301 csd1 >>> --sim-sign pos --seed 6555731749 >>> >>> I always get the following error: >>> >>> ERROR: you must supply --fwhm with --sim, even if it is 0 >>> >>> Is there a bug in the mri_glmfit function? >>> >>> Thank you all in advance, >>> Rafael. >>> _______________________________________________ >>> 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 >> >> >> >> 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. >> >> >> > > > -- 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
