On 10/25/11 10:57 , Steph Bickel wrote:
> Hi Rudolph,
>
> thanks for your speedy response.
> I want to get distance along vertices (the surface) between two vertex
> points.

OK -- 'mris_pmake' works for this. Say you have a subject called 'test'
and you want to calculate the distance on the lh 'smoothwm' from vertex
1000 to 20000:

mris_pmake --subject test --hemi lh --surface0 smoothwm --surface1
smoothwm --curv0 curv --curv1 curv --mpmProg pathFind --mpmOverlay
distance --mpmArgs startVertex:1000,endVertex:20000

The only important options are '--surface0 smoothwm --mpmProg pathFind
--mpmOverlab distance --mpmArgs startVertex:1000,endVertex:20000'

The other args, '--surface 1 smoothwm --curv0 curv --curv1 curv' are not
used for finding the path, but do nonetheless need to be filled in. As I
indicated, "mris_pmake" is more developer than user friendly.

So, the above will generate in your terminal:

Start->End vertices                                    [ 1000->20000 ]
Total path cost                                          [ 55.957047 ]
LabelWrite: saving to ./dijk.label

Where the "Total path cost" corresponds to the distance along the mesh
(using the "distance" overlay in the "pathFind" module between vertices
1000 and 20000 means that the minimum cost in moving between those
locations is the minimum distance).

You can load the 'dijk.label' into Freeview to see the path itself.

If you want to use the 'inflated' surface instead, change the arg to
'--surface0':

mris_pmake --subject test --hemi lh --surface0 inflated --surface1
smoothwm --curv0 curv --curv1 curv --mpmProg pathFind --mpmOverlay
distance --mpmArgs startVertex:1000,endVertex:20000

which outputs:

Start->End vertices                                    [ 1000->20000 ]
Total path cost                                          [ 57.521545 ]
LabelWrite: saving to ./dijk.label

Oh, and I have a strong suspicion that you need to use the current 'dev'
version of 'mris_pmake'. If you are using the 'stable' version and it
won't work, let me know and we can get the 'dev' version out to you.

Best
-=R



--
Rudolph Pienaar, M.Eng, D.Eng / email: rudolph@nmr....
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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