Hello dear FreeSurfer team,
We are undertaking a multicenter study analyzing cortical thickness of controls and persons with a neurological condition. Unfortunately, there are issues with motion artifacts and image quality. To counter this, we’ve created averaged T1-images by combining one axial and one sagittal image in SPM for one of the study sites. Also, we are using recon-all with the optional T2- and T2-pial flags. Our impression is that the image quality has improved with the averaged images as compared to the non-averaged ones.
Do you have any thoughts on this method or if combining images this way might cause issues when trying to calculate and compare cortical thicknesses? The averaged T1-images are only created for one of the study-sites and we plan on using study site as a covariate in our model. Will be happy to post images or logs if those may be helpful
Kind regards,
Carl
FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Platform: CentOS Stream 8