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 fischl@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 matt@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" cschwiedrz@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
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