It will behave differently as some of the parameters change depending upon whether it is a T2 or FLAIR. This will only affect the surface creation

On 02/02/2017 05:19 PM, Joe Necus (PGR) wrote:

Hello,

I am running recon-all on the latest version of freesurfer (Version 6) and would like to know whether there is any difference between using the -T2 -T2Pial and -Flair flags.

I am currently running recon-all with a T1 and FLAIR image, but have used the -T2 -T2pial flags and would like to know whether I need to go back and instead re-run with the -FLAIR flag instead.

Thanks a lot,

Joe

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