You will definitely get systematic differences between using T2 and not, so you could have a false positive (or negative) if you are comparing those two groups. On the other hand, you probably changed the T1 protocol a lot between now and 10 years ago, so you are likely to have bias either way.

On 2/11/2022 12:53 PM, Eszter Boros wrote:

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Dear FreeSurfer Team,

We have collected T1 and T2 images in our study and running recon-all with T2 gives us much better results (it was really good to see it).

Our aim is to compare these structural data (in Group A) to another patient group (Group B). The problem is that the data of Group B was collected 10 years ago and we did not have a T2 in that study.

I am wondering what would be the best approach? Maybe we should not use T2 in Group A because we do not have a T2 in Group B? Or if we do the manual corrections correctly in Group B, this should not be a problem?
I am using Freesufer 7.1.1

Thank you for your answer! I greatly appreciate it.

All the best,
Eszter Boros

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