Dear FreeSurfer experts,

 

I have both T2 and FLAIR images for the majority of the subjects in my study,

and I want to use them to improve pial surface reconstruction during recon-all

as explained in [1].

 

My questions are:

 

1) In general, should I prefer FLAIR over T2, or the other way around?

2) Some subjects (< 10%) do not have a FLAIR image, and others do not have a

T2. Do you think that it is fine to use FLAIR for some subjects, and T2 for others, in the same study? We will perform manual QC after the recon-all run and exclude bad quality images so I wanted to hear your opinion.

 

Best,

 

VB