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 herehttps://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Other:

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 -autorecon2?

I think the answers are yes because -T2 appears under -autorecon3 only in ReconAllDevTablehttps://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable.

Best, Tashrif

-------------------------------------------------------------

Tashrif Billah, MS

Research Engineer

Brigham and Women's Hospital

Harvard Medical School

tbillah@bwh.harvard.edumailto:tbillah@bwh.harvard.edu

http://pnl.bwh.harvard.edu/tashrif-billah-m-s/

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