rh.pial.T1 is the T1-based surface, rh.pial.FLAIR is the FLAIR-based surface refined from the T1 surface. rh.pial is the final surface and is a symbolic link to rh.pial.FLAIR
On 9/10/2020 10:40 AM, Otília C. d'Almeida wrote:
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Hi FS community,
I started using FS 7.1.0 for cortical and subcortical parcellation/segmentation.
As I found information that FLAIR data could improve pial surfaces creation, I decided to try it on since I have FLAIR images besides MPRAGE, by using the command line form FSwiki:
*recon-all -subject NAME -i input_volume.nii -FLAIR FLAIR_volume.nii -FLAIRpial -all*
However when I opened Freeview, I overlaid *rh.pial*, and *rh.pial.FLAIR, rh.pial.T1*.
The first two are quite similar (overlap) and the segmentation is worse than rh.pial.T1.
So, my question is, what is really the final surface of recon-all that must be checked for errors and that is used for stats estimation?
Thank you in advance.
Best regards,
Otília
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