Hi Bruce, if i have analyse format which is the right orientation to enter the data in freesurfer. Radiologically (r/l) or vise versa? John
On Thu, Nov 6, 2014 at 3:21 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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:
- recon-all -autorecon1 -subjid
edit pia, save brainmask.mgz recon-all -autorecon2 -autorecon3 -subjid
- recon-all -autorecon1 -autorecon2 -subjid
edit pia, save brainmask.mgz recon-all -autorecon2-pial -autorecon3 -subjid (preferred)
- recon-all -subjid
edit pia, save brainmask.mgz recon-all -autorecon-pial -subjid
Please comment, thank you, Octavian
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