Hi Yuko, it should be performing Gaussian Random Field (GRF) cluster-wise correction. Based on the smoothness, the size of the search space, and the voxel-wise threshold, it attempts to compute the p-value of resulting clusters. The differences between GRF and doing the simulation are that GRF runs almost instantly but it can be inaccurate at low smoothnesses and low thresholds. It looks like the GRF was not implemented until 5.1
doug yukoyy wrote: > Dear all, > > I'm conducting volume based group analysis and corrections for multiple > comparisons. > My environment :Mac OS 10.6.8, Freesurfer 5.0.0 > > I followed the instruction I found here: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel > > When I first successfully ran: > mri_glmfit --y ces.005.nii --wls cesvar.005.nii --osgm --glmdir F2glm.wls > --nii.gz > tkmedit fsaverage orig.mgz -aparc+aseg -overlay F2glm.wls/osgm/sig.nii.gz > -fminmax 3 7 > > Then, I wanted to do corrections for multiple comparison. > mri_glmfit-sim --glmdir F2glm.wls --grf 3.0 pos --cwpvalthresh .0166 > > However, FreeSurfer does not seem to recognize --grf, and I don't understand > what does grf do. > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > ERROR: Flag --grf unrecognized. > --glmdir F2glm.wls --grf 3.0 pos --cwpvalthresh .0166 > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > I chose to use --grf because it was suggested in the tutorial, and in > FreeSurfer mailing list archive. > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20573.html > > I am guessing that I cannot use --cache for volume analysis because I don't > have > /Applications/freesurfer/average/mult-comp-cor/fsaverage/volume/cortex/fwhm12/pos/th30/mc-z.csd > > I also tried monte-carlo simulation, and it worked okay. > > So, here is my question. > What does --grf do? and Is there any documentation? > > Thank you! > Yuko Yotsumoto > yuk...@a7.keio.jp > _______________________________________________ > 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.
