it is hard to tell from that view. Can you click on a point that appears to be outside the brain so we can see what it looks like around that point in all three views?
On 01/15/2016 10:56 AM, Xiaomin Yue wrote: > Hi All, > > In fs5.3, I tried to generate a volume mask from the pial surface > using mri_surf2vol: mri_surf2vol --mkmask --hemi lh --reg > $subjsess/bold/001/register.dof6.dat --template > $subjsess/bold/001/template.nii --surf pial --o > $subjsess/bold/001/lh.pialmask.vol.nii. The command run successfully. > I doubled check the registration between the EPI and high resolution > T1.mgz under the $SUBJECTS_DIR, which has the mincost at 0.3898. > however, when I overlaid the mask on the T1.mgz, it is clear that > some voxels outside brain are in the mask, and some voxels in the gray > matter are not in the mask (see attached figure). Did I use the > function incorrectly? > > Thanks very much for your help. > > Xiaomin > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
