To answer #2, You should definitely not mix them. For #1, the study has not been done. In principle, FLAIR is better because T2 has both bright and dark in the extra cerebrum whereas FLAIR has only dark. That said, there might be other factors that could make FLAIR worse.

On 7/20/2020 12:13 PM, Batra, Vinita R. wrote:

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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

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