Try this first
mri_cor2label --c aseg.mgz --id 17 --l lh.hippo.label
Then load lh.hippo.label

If wramygdala.R.001.nii is not in the conformed space, your command will
not work

On 04/04/2014 05:17 PM, Cherisse Onuigbo wrote:
> mri_cor2label --c wramygdala.R.001.nii --id 1 --l wramygdala.R.001.label
> tkmedit Subjects_for_Cherisse/S001 T1.mgz -aux brainmask.mgz -seg aseg.mgz
>
> And then I added the label using the drop down menu.
> On Friday, April 4, 2014 3:45 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu> wrote:
>
> 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 <mailto: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>
> <mailto: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
> > >
> > > >
> > > >
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
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> > >
> > > --
> > > 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>>
> > <mailto: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
> > >
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> > > Outgoing:
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> > >
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