If I understand correctly, you have one site that acquires two scans, one sag and one axial, and you want to register them together and compute the average, then feed the average to recon-all? Do they have the same isotropic resolution? I'd guess that this would create a systematic artifact.

On 8/3/2022 3:17 PM, Trolle, Carl wrote:

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

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