Hi Caspar is the closest white matter captured by the white surface? What is the intensity of voxels there? If < 110 you could try putting control points in them and seeing if that helps (that is, in the closest voxels that are entirely white matter).
Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: > Hi Bruce, > ok. > But in theory, what would you recommend to get around the darkening > issue? Unfortunately, I do not have a field map available for this > data set. > Or should I not expect to get a pial surface in this area since the > white matter is not discernable? > There are five slices without clear white matter (original voxel size > 0.5x0.5x0.5 mm). > Thanks, Caspar > > 2013/5/16 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >> Hi Caspar >> >> if it's primate I don't think I'm going to be able to help - you'll need >> someone more familiar with primate anatomy >> >> sorry >> Bruce >> On Thu, 16 May 2013, Caspar M. >> Schwiedrzik wrote: >> >>> Hi Bruce and Matt, >>> yes, it is primate data. I just dropped an archive on your FTP server >>> in transfer/incoming. >>> Thanks! >>> Caspar >>> >>> 2013/5/16 Matt Glasser <m...@ma-tea.com>: >>>> Is the brain extraction removing that part of the brain? Do you know >>>> where the OFC ends and olfactory bulb begins? >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> On 5/16/13 11:43 AM, "Caspar M. Schwiedrzik" >>>> <cschwie...@mail.rockefeller.edu> wrote: >>>> >>>>> Hi! >>>>> I am failing to get a proper pial surface in orbitofrontal cortex. >>>>> See attached screenshot. >>>>> This is NHP data, processed with version 4.5. >>>>> I am not sure how to proceed here, as there is no clear with matter. >>>>> Any advice would be appreciated. >>>>> Thanks! >>>>> Caspar >>>>> _______________________________________________ >>>>> 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
