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,2012/4/5 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
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
<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:Freesurfer@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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MGH-NMR Center
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