Hi all

I am running Freesurfer 7.4

I use recon-all with the -FLAIRpial option.

1) I wonder whether the FLAIR to T1 registration is handled by recon-all or whether I need to supply a FLAIR image already registered to T1.

2) in case recon-all handles the registration, is there a way I can check the registration quality? which file should I use in freeview?

3) in case I already have a reliable FLAIR to T1 registration, is there a way to make recon-all skip the FLAIR to T1 registration?

In addition, I would like to use segmentHA_T2.sh

4) in case recon-all handles the registration, which file can I give to segmentHA_T2 as additional scan? I guess I should select the FLAIR already registered to T1..

5) Is there a reason why I should prefer a T2 image to a FLAIR for segmentHA_T2?

Thank you

Simone Cauzzo, PhD

University of Padova