Re: [Freesurfer] notal-check/pial edits

2014-11-06 Thread Octavian Lie
I subscribe to the question above. Also, is there a flag that would make recon throw a warning about tailarach registration issue, but not stop the routine? Thank you, Octavian On Thu, Nov 6, 2014 at 7:30 AM, John Epiktitos wrote: > Hi Bruce, > if i have analyse format which is the right orien

Re: [Freesurfer] notal-check/pial edits

2014-11-06 Thread John Epiktitos
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 wrote: > Hi Octavian > > does your data show in the proper orientation in freeview/tkmedit? Analyze > is a dang

Re: [Freesurfer] notal-check/pial edits

2014-11-06 Thread Bruce Fischl
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 run

[Freesurfer] notal-check/pial edits

2014-11-05 Thread Octavian Lie
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