Sorry, I was thinking that my question may not have been very clear. Baseline T1 images were rigidly registered to 1mm^3 MNI template and then all follow-up images were rigidly registered to the individual's baseline T1. My question is whether I could still apply the Freesurfer longitudinal pipeline (i.e. using recon-all -base <templateid> -tp <tp1> -tp <tp2> -all) to these images as they are (i.e. rigidly registered to the baseline scan) or if you had any guidance as to how to best proceed.

thank you in advance and sorry to email twice!

Kathleen

On Thu, Nov 29, 2018 at 6:35 AM kathleen Gerbino <kathleen.gerbino@gmail.com> wrote:

Hi FreeSurfer experts:

I hope you are well. I need to segment quite a few longitudinal T1 scans from patients with multiple sclerosis. A colleague has applied an automated lesion segmentation algorithm to segment and fill the lesions. During this process, the follow-up scans were registered to the baseline scan. My question is whether I could still apply the Freesurfer longitudinal pipeline to these images or whether your had any recommendations on the appropriate steps to take if this is not appropriate.

Kind regards,
Kathleen