Yes, the T2 is only used to refine the pial surface

On 11/26/2019 5:14 PM, Billah, Tashrif wrote:
Hi all,

Is -T2 used only in -autorecon3 as shown 

recon-all -subject subjectname -T2 /path/to/T2_volume -T2pial -autorecon3

In other words, if I do:

recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume 
-T2pial -all

Will only -autorecon3 make use of the provided -T2 and not -autorecon1 or 

I think the answers are yes because -T2 appears under -autorecon3 only in 



Tashrif Billah, MS

Research Engineer

Brigham and Women's Hospital

Harvard Medical School<>

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