[Freesurfer] differences between mri_glmfit and intergroupavg-sess

Hello,

I've comparing results of output from intergroupavg-sess with output from mri_glmfit, and the difference seems to be too huge to be accountable just from differences between the two programs.

I attached images that go along with the commands below. What do you think could be the cause of these huge differences? Are there any parameters that might reduce the difference?

Thanks, Rob

(September 2005) intergroupavg-sess \ -group1 BwGroupNormalsError5 \ -group2 BwGroupAspError5 \ -space sph \ -spacedir sph_sm20 \ -intergroup BwGroupError5 \ -analysis EMerror \ -contrast ASevASc

(Currently ran this because so I could then adjust the threshold using monte carlo data. The results of this should I think be the same or similar to the intergroupavg results) /space/greve/1/users/greve/freesurfer/bin/mri_glmfit \ --really-use-average7 \ --y rh.ASevASc_8s_BwGroupError5.fsfast.mgh \ --fsgd fsgd_and_contrast_files/BwGroupError5.fsgd \ --glmdir rh.ASevASc_8s_BwGroupError5.fsfast.glmdir \ --pca \ --surf average7 rh \ --C fsgd_and_contrast_files/BwGroupError5.mat \ --label average7/label/dACC_rACC_final-rh.label \ --fwhm 4.6