Yes, that should work, except you will need to add --perm-resid. See the --help
On 09/13/2017 02:33 PM, Martin Juneja wrote: > Hi experts, > > To calculate simulations on LGI measures, I ran: > mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 permcsd > --sim-sign abs --cwpvalthresh .05 > > But it gives error: ERROR: design matrix is not orthogonal, cannot be > used with permutation. > > I came across a post where its mentioned that: > "Alternatively, I have a version of mri_glmfit-sim that will run > permutation with non-orthogonal designs. > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim > <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim>" > > - Douglas N. Greve > > So I was wondering if I can use this program for LGI measures and run > the same command, lets say this new program is: mri_glmfit-sim_new, so > can I run the following command (instead of doing PALM): > > mri_glmfit-sim_new --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 > permcsd --sim-sign abs --cwpvalthresh .05 > > Thanks. > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
