Thanks. Xiaomin
On Fri, Jan 15, 2016 at 11:41 AM -0800, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: or you can add --fillribbon to your surf2vol command (but the label2vol method is probably better) On 01/15/2016 12:32 PM, Xiaomin Yue wrote: > Maybe, I misunderstand it. Is the pial surface same as gray matter? > If not, how could I create a gray matter mask? > > Thanks, > > Xiaomin > > > > > On Fri, Jan 15, 2016 at 9:31 AM -0800, "Douglas N Greve" > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > I think you could easily hit all those voxels with a 1.5mm voxel size. > Not sure what you are asking about in terms of gray matter. > > On 01/15/2016 12:27 PM, Xiaomin Yue wrote: > > The voxel size is 1.5mm. Some of voxels in the gray matter are not > > included in the mask as well. Why? > > > > Xiaomin > > > > > > > > > > On Fri, Jan 15, 2016 at 9:21 AM -0800, "Douglas N Greve" > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > That point is fairly close to the pial surface. What is your voxel size? > > It will include any voxel even if only a corner of it has some surface > > in it. > > > > On 01/15/2016 12:16 PM, Xiaomin Yue wrote: > > > here it is. thanks, > > > > > > > > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > From: gr...@nmr.mgh.harvard.edu > > > > Date: Fri, 15 Jan 2016 12:00:02 -0500 > > > > Subject: Re: [Freesurfer] mri_surf2vol {Disarmed} > > > > > > > > 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 > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://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. > > > > > > > > > > > > > _______________________________________________ > > > 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 > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://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 > > > > > > _______________________________________________ > > 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 > <http://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 > > > _______________________________________________ > 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
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