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 <epikti...@gmail.com> wrote: > 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 <fis...@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: >>> >>> 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 >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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