If you want to use GRF, you should use smooth by twice the native voxel size. I would not go higher than .01 on the threshold doug
On 01/26/2014 12:52 PM, Susan Ruiz wrote: > Hi FreeSurfers, > I was just reading this post to the archive (below) regarding using > mri_glmfit-sim > on volume data, and it suggests that using --grf rather than doing the > simulation > can be "inaccurate at low smoothness and low thresholds." > At what smoothness values and threshold values should we opt to use the > simulation over GRF for volume-based cluster corrections? > Thanks, > ~Sue Ruiz > > > 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 at a7.keio.jp > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > />/ _______________________________________________ > />/ Freesurfer mailing list > />/ Freesurfer at nmr.mgh.harvard.edu > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > />/ https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > />/ > />/ > />/ > / > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve at nmr.mgh.harvard.edu > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > -- > * * ** *** ***** ******** ************* > Susan Mosher Ruiz, Ph.D. > Research Scientist > Boston University School of Medicine > Laboratory of Neuropsychology > VA Boston Healthcare System > smos...@bu.edu <mailto:smos...@bu.edu> > * * ** *** ***** ******** ************* > > > _______________________________________________ > 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.
