I have subject proceed with Freesurfer 4.30 and Freesurfer 5.1. The subjects proceed with Freesurfer 5.1 appears to have thicker cortex than in Freesurfer 4.30. When I correlate the cortical thickness against continuous variables like IQ, I get a difference. Is this expected since I get a correlation on the different side with Freesurfer 4.30 and Freesurfer 5.1.? Can part of the explanation be that Freesurfer 5.1 does not use mri_gcut, and that the registration transformation is changed in Freesurfer 5.1? I get different ras_vox matrix transformation and different flip angle.

Knut J