[Freesurfer] MS Lesions effects on cortical thickness in FS 6.0

Dear Freesurfer experts,

We are facing a problem in our study and would need your advice on it. We want to get an accurate measurement for the cortical thickness from our MS patients data. For that we are using 3D T1 and FLAIR (recon-all will be used with the FLAIR option so that we can a more accurate pial surface). However, we were wondering if running recon-all on the raw data would lead to some errors specially because of the juxtacortical lesions or not. Or, is it better to first apply a lesion filling using our lesion mask ? I should specify that we will use the longitudinal pipeline if it is of any use.

Thank you all.

Ismail

PhD candidate Neurocentre Magendie, INSERM Bordeaux, France