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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-all -s x autorecon2-wm -autorecon3 -T2 volT2.nii -T2pial
If so, can I obtain similar results with mri/orig/T2 raw.mgz instead of the volT2.nii input? Thanks, OL
On Mon, May 4, 2020 at 10:49 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
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:
External Email - Use CautionDear 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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