Hi
By default, the output is a ascii text file. If you want the output to be a surface file, you need to use the option "--surfout".
I am not sure if it will be compatible with freeview though, so let me know if that works or not.
Note that you could also have used the "--fopd" option in probtrackx2 to record streamlines directly on the surface [assuming you are running as command line].
Cheers
Saad
On 25 Oct 2012, at 14:55, Bastian Cheng wrote:
> Dear fsl-experts,
>
> I am trying to project connection probabilities onto a freesurfer cortical surface.
>
> As I understand from the documentation (built 501), surf_proj should be the right tool.
>
> My data:
>
> paths_fnirt: fdt_paths fnirted to freesurfer space (checked, fits on brain.nii.gz from freesurfer recon.)
> lh.white.asc: converted brain surface file (checked in freeview)
>
> So I used:
>
> surf_proj --data=paths.nii.gz --surf=lh.white.asc --meshref=brain.nii.gz --out=testproj
>
> (I might not need the --xfm option since my 3D data is already in the same space as the reconstructed brain surface.)
>
> Everything works well and I get an ascii-file. However, I cannot open this file either with freeview, tksurfer or tkmedit.
>
> I could also upload the output file ("testproj")
>
> Somehow I was expecting to get a cortical surface file that could be color-coded for connection probability. But am not sure if my approach is feasible...
>
> I would appreciate any help!
>
> All the best,
> Bastian
>
>
> PS. output of surf_proj
>
> read data
> read surface
> nz=141634
> nnz=0
> project data
> save
> numda2 3
> write vertcies 141634
> write traingles 283264
> 283264 141634
> resize trinagle array
> write faces 849792
> scalar 0 2
> set scalar names 1 MyScalars
> do memcpy
> scalar int 0
> done scalar
> null
>
--
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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