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 greve@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 greve@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.