On Tue, Apr 17, 2012 at 5:52 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Can you run the following?

mri_surf2vol --mkmask --hemi rh --fillribbon --identity sub01 --template
subj01/mri/orig.mgz --o surf-mask.nii
tkmedit sub01 orig.mgz -overlay surf-mask.nii -fthresh .5

this should just create a mask of the rh surface in the volume. If this
fails, then there's something wrong with the subject data.

doug

On 04/17/2012 03:43 AM, René Besseling wrote:
> That gives the same scattered appearance as before, see attachment. So
> I guess it's not a viewer issue. Maybe something to do with missing
> header information of the original T1 scan?
> By the way: strange that the overlay contains so many zeros; one would
> expect (transparent) NaNs...
>
> Best regards,
>
> Rene
>
>
> On Thu, Apr 12, 2012 at 7:38 PM, Douglas N Greve

> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> Try loading it in tkmedit, something like:
>
> tkmedit sub01 orig.mgz -overlay sig_2subj01_volumetric.nii
>
> doug
>
>
> On 04/12/2012 03:46 AM, René Besseling wrote:
>
> Hi Doug,
>
> Sorry, missed your reply. I assumed the --identity argument
> was used for looking up the surface-to-volume mapping
> somewhere in the predefined folder structure of this subject.
> Anyhow, my last command was
> mri_surf2vol --surfval sig_2subj01.mgh --hemi rh --fillribbon
> --identity sub01 --template subj01/mri/orig.mgz --o
> sig_2subj01_volumetric.nii
> so I guess no transformation is needed since the surface is
> already in the proper space (that of subj01).
> About my tkmedit command: I'm not using that. I usually
> visualize my results in Matlab, for the pics I send I used
> Freeview and tksurfer (so commands such as "mrview T1.mgz" and
> "tksurfer fsaverage lh inflated")
> Best regards,
> René
>
>
> 2012/4/5 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>>>
>
>
> The template specifies the output geometry. When you specify
> --identity, you specify a particular transformation between the
> volume and the surface, so you can't change the target volume
> without specifying a different transform. I'm at a bit of a
> loss
> as to why this is not working. What is your tkmedit command?
> doug
>
>
> On 04/05/2012 06:04 AM, René Besseling wrote:
>
> Hi Doug,
>
> I'm using tksurfer to visualize the surface maps; this
> looks
> OK for both the original map overlaid on fsaverage and the
> mapped surface (generated using mri_surf2surf) overlaid on
> subj01. The mapping from surface to cortical ribbon
> also works
> well for fsaverage but goes haywire for subj01, see pics in
> attachment.
>
> I noticed that mri_surf2vol gives different results
> when using
> different --template volumes. Why is that? I assumed
> that the
> --template image essentially provides the range of voxel
> coordinates to which the surface values can be mapped. In
> other words: when providing a template with a bigger
> field of
> view, I'd expect the center of the resulting output to look
> the same as the output generating when using a small FOV
> template. Does it matter whether you write your output
> as .mgz
> or .nii?
>
> Best regards,
>
> Rene
>
> On Wed, Apr 4, 2012 at 10:42 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>>
> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
>
> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>> wrote:
>
> How are you visualizing the results? Can you send a pic?
> You should be
> using tkmedit.
> doug
>
> On 04/04/2012 09:59 AM, René Besseling wrote:
> > Dear Freesurfer users,
> >
> > I've been trying to map a Qdec contrast sig.mgh to the
> native volume
> > of a subject using mri_surf2surf (to get from Qdec fsaverage
> surface
> > to native surface) and mri_surf2vol (to map from native
> surface to
> > native volume cortical ribbon). However, the last step goes
> wrong: I
> > get a nii with the same range of values as were in the
> surface, but
> > the nonzero voxels are scattered all over, so I guess there is
> > something wrong with the surface-to-voxel coordinate mapping.
> Below is
> > my code, any ideas on what goes wrong?
> >
> > Best regards,
> >
> > Rene
> >
> > mri_surf2surf --hemi rh --srcsubject fsaverage --noreshape
> --sval
> > sig.mgh --trgsubject subj01 --tval sig_2subj01.mgh
> >
> > mri_surf2vol --surfval sig_2subj01.mgh --hemi rh --fillribbon
> > --identity sub01 --template subj01/mri/orig.mgz --o
> > sig_2subj01_volumetric.nii
> >
> >
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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>>
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>
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> -- Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@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>
> Phone Number: 617-724-2358 <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu

Phone Number: 617-724-2358
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