On 11/12/2024 6:58 AM, Simone Cauzzo wrote:

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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.

Recon-all does it

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?

There should be a .log file produced by bbregister. If you look at the end of that, you will see a tkregisterfv command that will allow your to check the quality (tkregisterfv is a frontend for 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?

No, not really. In theory, you could copy your registration over the one produced by recon-all, but I think it would get overwritten. There might be a way around this with expert options. But check the output of recon-all because it is generally very good.

In addition, I would like to use segmentHA_T2.sh

I'll leave these for @Eugenio

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

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