Hi Tyler
Do you have scalars associated with your surface vertices that are set to zero? If that is the case they may be ignored by surf2surf.
Saad
On 29 Apr 2012, at 21:42, Tyler Blazey wrote:
> Hi List,
>
> I have been trying to use the new surf2surf tool that comes as part of the probtrackx2 pre-release to convert a FIRST vtk surface into FreeSurfer asc. My command line input is:
>
> surf2surf --surfin=first_inputs.txt --surfout=freesurfer_outputs.txt --convin=first --volin=first_T1.nii.gz --convout=freesurfer --volout=freesurfer_T1.nii.gz --xfm=first_to_freesurfer.mat
>
> This exits without any sorts of errors, but when I view the resulting surface in tkmedit, it only marginally encloses the intended region. I have also confirmed this by using the converted surface as both a seed and stop mask in probtrackx2. There isn't any problem with my transformation, 'first_to_freesurfer.mat', so I am not sure what the issue is. Any ideas?
>
> Thanks,
>
> -Tyler
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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