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 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.
