External Email - Use Caution
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