Hi Kathleen,

if you map one image to the other, this introduces interpolation artefacts, which will bias your analysis (any type of analysis, so this is already a problem in the lesion segmentation part).

Technically you run longitudinal freesurfer on these images but (similar to the lesion analysis) you will never know if changes across time are due to the processing bias or if they are real.

Get the original data, not the mapped images, and work with those. (And you may want to warn your colleague that lesion change estimates are probably biased, if one image is mapped to the other).

Best, Martin

On Thu, 2018-11-29 at 11:50 -0500, kathleen Gerbino wrote:

External Email - Use Caution         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@gm ail.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

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