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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