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:
Here is the command: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?
mri_glmfit-sim --glmdir r_PCC_glm --grf 1.3 pos --cwp 0.05 --2spaces
Thanks,
Jiahe
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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.