find the angle between the vectors connecting each point with (0,0,0).

compute the fraction of the circle that it represents, and multiply it by:

K * PI * D

where

D = diameter of ?h.sphere
K = sqrt(surface area of surface you are interested in)
     ---------------------------------------------------
     sqrt(surface area of sphere)

cheers
Bruce

On
Tue, 25 Oct 2011, Steph Bickel wrote:

> Hi Rudolph and Bruce,
> thanks for your responses. 
>
> rudolph, your example works great. just 2 questions: 
> what dimension is the total path cost in the mris_pmake output? 
> is there a way to input a file with several vertex point pairs to compute
> the distance between, or do I have to loop through the pairs I would like to
> compute?
>
> Bruce, thank you very much for your suggestion. it would be easier for me to
> compute it this way and I would like to compare results with mris_pmake
> results. I am currently looking for a way to compute the distance on the
> sphere, if you have a suggestion how to do this it would be much
> appreciated.  
>
> Thank you,
>
> Stephan
>
>
> On Tue, Oct 25, 2011 at 2:26 PM, Rudolph Pienaar
> <rudolph@nmr....> wrote:
>       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
>
>
> The information in this e-mail is intended only for the person to whom
> it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
>
>
>
>