Re: [Freesurfer] use and registration of FLAIR in recon-all and segmentHA

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Dear Douglas Thank you for the kind response I was wondering if Eugenio had the chance to look at this issue thank you Simone Cauzzo

On Tue, Nov 12, 2024 at 12:58 PM Simone Cauzzo cauzzo.simone@gmail.com wrote:

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