You can just run
recon-all -s x autorecon2-wm -autorecon3 -T2pial
When you ran it the first time, your volT2.nii was copied into the
subject's folder and will be used when the pial surface is placed when
you include -T2pial
On 5/16/2020 1:12 PM, Octavian Lie wrote:
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Dear Doug
Just to be clear
I ran the 1st process on subject x with
recon-all -s x -T2 volT2.nii -T2pial
It still needed wm edits. On rerun, can I just do
recon-all -s x autorecon2-wm -autorecon3
or I need to reuse the T2 for best results
recon-
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
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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 t
