Recon-all does itExternal Email - Use Caution
Hi allI am running Freesurfer 7.4I 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.
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)
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?
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.
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?
I'll leave these for @Eugenio
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, PhDUniversity of Padova
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