That makes sense. And thanks for the suggestion! I tried running permutation test with the following command: mri_glmfit-sim --glmdir r_PCC_glm --sim perm 10000 1.3 perm.abs.1.3 --sim-sign abs
The results are empty maps for all the contrasts I have, which I did not expect, since some of the contrasts are simply testing group mean against 0. Any clue why that might be? Also, if I want to run one-tailed test using 'pos', how do I rewrite the above command to include the no-sim part? This didn't seem to work: mri_glmfit-sim --glmdir r_PCC_glm --sim perm 10000 1.3 perm.pos.1.3 --sim-sign pos --no-sim perm.abs.1.3 On Wed, Jul 19, 2017 at 3:21 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > Yes, that is expected with your command line. The issue is that you are > using a positive (pos) a priori hypothesis about the sign of the effect. By > default, freesurfer generates unsigned statistics (this is what you see > when you just view the stats map). When you specify pos, it adjusts the > voxel-wise sig value to that of the (lower) signed test, so you see more > voxels. > > btw, the cluster forming threshold that you are using (1.3 = p<.05) is too > small for GRF. Probably you need something like 3 (p<.001). If you want to > use 1.3, then use permutation. > > On 7/19/17 2:56 PM, Jiahe Zhang wrote: > > Dear Freesurfer experts, > > I'm trying to run multiple comparisons correction using mri_glmfit-sim. > Since I'm working with volume data, I used -grf instead of -cache. The > resulting map has bigger clusters with higher significance values than the > original sig.mgh map from mri_glmfit. Is this normal? Is there anything I > should change in my command? > > Here is the command: > mri_glmfit-sim --glmdir r_PCC_glm --grf 1.3 pos --cwp 0.05 --2spaces > > Thanks, > Jiahe > > -- > Jiahe Zhang > Ph.D. Candidate > Department of Psychology > Northeastern University > 617-373-4789 <(617)%20373-4789> > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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. > > -- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-4789
_______________________________________________ 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.
