Hi Octavian

does your data show in the proper orientation in freeview/tkmedit? Analyze is a dangerous format as it doesn't contain direction cosine info and hence even if it looks right you may have left/right swapped and not know it.

I don't think the spherical stuff needs tal, so if it runs through without it you are fine.

cheers
Bruce

On Wed, 5 Nov 2014, Octavian Lie wrote:

Dear All,

this is very basic. I have Analyze volumes, and I was suggested to use
-notal-check to bypass the 3rd recon step. I wanted to make sure skipping
the T registration step would not have the potential to mess up the
spherical registration in autorecon3 in any way on a case by case basis. I
do not want to spend time in tkregister2 unless is necessary for the
spherical registration step.

Also, I anticipate losts of pial edits (let's exclude the wm edits/cp), and
I wanted to make sure different command scenarios are correct:

1. recon-all -autorecon1 -subjid
edit pia, save brainmask.mgz
recon-all -autorecon2 -autorecon3 -subjid

2. recon-all -autorecon1 -autorecon2 -subjid
edit pia, save brainmask.mgz
recon-all -autorecon2-pial -autorecon3 -subjid
(preferred)

3. recon-all -subjid
edit pia, save brainmask.mgz
recon-all -autorecon-pial -subjid

Please comment,
thank you,
Octavian

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