Dear freesurfer experts,

 

I am performing a longitudinal study (2 time points, 1 year apart) in patients with Multiple Sclerosis using freesurfer 6.0.

 

After following the tutorial for the CROSS, the BASE (where I only performed few manual edits of the surfaces) and the LONG steps, I am facing a problem with the results of the longitudinal pipeline:

 

If I overlay the final surfaces of the different time points (the white and pial surfaces of the LONG step) on the BASE template, there are major differences between the two time points (see figure attached). This happened only on a subset of my subjects.

One of our collaborators in this study suggested that this might be because the patient was positioned differently in the two time points, in particular with respect to the z axis (and indeed the major differences between the two surfaces are in the topmost area of the brain).

Does anybody have experienced the same problem? And how can I correct for it?

 

Thank you in advance for your help.

(*in the capture surfaces of the first visit are in yellow and in green for the second visit)