Thank you Doug. So, instead of running mri_surfcluster I should run mri_glmfit-sim with the --fwhm-override with the smoothing obtained from the residuals of the lme model.
Thanks again, A 2017-07-18 22:09, Douglas N Greve escrigué: > Not sure. It might be more accurate. Once you have the FWHM you want, > you can run mri_glmfit-sim with --fwhm-override > > > On 07/17/2017 05:43 PM, Jordi Pegueroles wrote: >> Dear FS experts, >> >> I was wondering if someone had performed multiple comparisons (ie >> monte-carlo) with the LME analyses. I have found a thread >> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40195.html) >> where Doug recommends to run a GLM fit with the same data and then >> overwrite the sig.mgh file with the LME one. >> >> My question is if is not more accurate to estimate the residuals from >> the LME model, then compute the relative smooth of the data with the >> mris_fwhm command and pass it as an argument in the mri_surfcluster >> command (mri_surfcluster --in $direct1/sig.mgh --csd >> /Applications/freesurfer/average/mult-comp-cor/fsaverage/${hemi}/cortex/fwhm${rfwhm}/abs/th13/mc-z.csd >> >> --cwsig $direct1/mc.abs.th13.sig.cluster.mgh --vwsig >> $direct1/abs.th13.sig.vertex.mgh --cwpvalthresh 0.05 --surf white). >> >> Thanks in advance. >> > > -- > 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/ > > > > 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. -- Jordi. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
