[Freesurfer] using T2 for recon-all

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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