Hi
I would recommend using probtrackx2 for this, as unlike probtrackx, you don't need a surface description: probtrackx2 does not assume that you are using just one surface, but instead each ROI mask defines its own surface.
If you need both hemispheres (e.g. one where the seed is and one where the waypoint mask is) then you should use both surfaces.
I am assuming your seed/target masks are freesurfer label files? In this case, you will need to transform these into surface files using label2surf (seed the doc)
Cheers
Saad
On 8 Oct 2012, at 05:38, Monica Giraldo wrote:
> Dear FSL experts, I'm trying to run tracktography between a region in left hemisphere to a region in the right one using freesurfer surfaces. I don't know what file to put as a description of the whole cortical surface. In FSL page you recommend lh.white.asc if Left hemisphere and rh...etc if right hemisphere .... But if I'm tracking in both hemispheres then what file I put? I see in the folder mri (from the output of freesurfer) a wm.mgz file but is not a label file.
> Sorry, I'm new with freesurfer. I was thinking on passing that .mgz to nifti as you tell to do with the brain.mgz in tutorial and use that but I'm not sure.
>
> Thanks,
>
--
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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