Sorry, our interface is a little bit confusing on this. Use -T2 to specify the T2 volume (eg, -T2 /path/to/T2.mgz). To apply the T2 to the pial use -T2pial (without any arguments)

On 5/2/2020 7:55 PM, Octavian Lie wrote:

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Dear All, 

I ran recon-all on the 1st run using the -T2pial flag. After wm.mgz edits, when running

recon-all autorecon2-wm -autorecon3 -T2pial volT2.mgz

it throws an error ~ 'flag volT2.mgz not recognized'. When reruning recon-all as above, do we need to include the T2pial flag to make use of the t2 pial information? If not, is the previous T2pial output used to regenerate the pia?

Thank you, 

OL

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