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 yukoyy@a7.keio.jp _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer