Try using Method 1 from this version of mri_surf2vol
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol
On 10/2/15 11:38 AM, Kevin Aquino wrote:
Ah sorry for not being clear,
Basically I would like the output from mris_surf2vol with the mask option to be less speckled.
For example, in the image attached: http://www.physics.usyd.edu.au/~aquino/example_mri_surf2vol.png http://www.physics.usyd.edu.au/%7Eaquino/example_mri_surf2vol.png
there are some voxels missing. Is there an option to fill these voxels?
Cheers,
*Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham.
Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney
*E* Kevin.aquino@nottingham.ac.uk mailto:Kevin.aquino@nottingham.ac.uk, aquino@physics.usyd.edu.au mailto:aquino@physics.usyd.edu.au | *W* www.physics.usyd.edu.au/~aquino/ http://www.physics.usyd.edu.au/%7Eaquino/
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On Fri, Oct 2, 2015 at 1:42 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Kevin I'm not clear on what you need. Would mri_surf2vol --fillribbon do what you want? I don't really know what else "voxelize" means cheers Bruce On Fri, 2 Oct 2015, Kevin Aquino wrote: Hi all, I am trying to "voxelize" the cortical surfaces generated in freesurfer and I am a little stuck. I have been using mris_surf2vol with the --mask option however this generates a very speckled representation of the cortical surface on the voxels. What I would prefer would be the level sets of the cortical surface interpolated onto voxels, even if they are at a different resolution that could be enough. Is this possible with any of the available commands? I also went down the route of mris_volmask however, this generates the cortical ribbon, which is something that I don't need. Cheers, Dr Kevin Aquino Research fellow, Sir Peter Mansfield Magnetic Imaging Center, School of Physics & astronomy, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney. E Kevin.aquino@nottingham.ac.uk <mailto:Kevin.aquino@nottingham.ac.uk>, aquino@physics.usyd.edu.au <mailto:aquino@physics.usyd.edu.au> | W www.physics.usyd.edu.au/~aquino/ <http://www.physics.usyd.edu.au/%7Eaquino/> ---------------------------------------------- The brain is a wonderful organ. It starts working the moment you get up and does not stop until you get into the office. - Robert Frost CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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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