What were your mri_cor2label and tkmedit command lines? SPM will never
work properly for what you are trying to do.

On 04/04/2014 04:42 PM, Cherisse Onuigbo wrote:
> I first checked it in tkmedit, but I didn't see the region in green as
> I went through the slices. I also put another label in there just to
> check if I was displaying labels correctly and others showed up. Then
> I used the display function in spm and input the coordinates there,
> but it showed that the coordinates were outside the region. Also I was
> wondering why in the label file, all of the vertex id's are -1 instead
> of what I specify in the command.
> On Friday, April 4, 2014 3:08 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu> wrote:
>
> How are you checking the vertex coordinates? You can't use SPM, you'll
> have to use tkmedit or freeview
>
> On 04/04/2014 04:04 PM, Cherisse Onuigbo wrote:
> > My mask is a volume mask. When I run the function normally, the
> > vertices that are in the text file do not fall in the region of my mask.
> > On Friday, April 4, 2014 2:28 PM, Douglas N Greve
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
> >
> > Hi Cherisse, i don't understand what you have done. Is the mask a volume
> > mask or surface mask? In mri_cor2label, you can specify a surface to get
> > surface vertex numbers.
> >
> > doug
> >
> > On 04/02/2014 07:03 PM, Cherisse Onuigbo wrote:
> > > Hello
> > >
> > > I was wondering how to create a label from a binary mask. I created a
> > > mask and then normalized it to the template space. When I tried to use
> > > mri_cor2vol, all the vertex numbers come out as -1. I understand that
> > > the vertex numbers should come out as -1, but when I entered the
> > > coordinates in the display function in spm, it was not in the region.
> > >
> > > Thank you,
> > > Cherisse
> >
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto: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.