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 
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 <gr...@nmr.mgh.harvard.edu
>         <mailto:gr...@nmr.mgh.harvard.edu>
>         <mailto:gr...@nmr.mgh.harvard.edu
>         <mailto:gr...@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
>         <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>         <mailto:gr...@nmr.mgh.harvard.edu
>         <mailto:gr...@nmr.mgh.harvard.edu>>
>         <mailto:gr...@nmr.mgh.harvard.edu
>         <mailto:gr...@nmr.mgh.harvard.edu>
>
>         <mailto:gr...@nmr.mgh.harvard.edu
>         <mailto:gr...@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
>         gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
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>            --     Douglas N. Greve, Ph.D.
>            MGH-NMR Center
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>     -- 
>     Douglas N. Greve, Ph.D.
>     MGH-NMR Center
>     gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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