Hi Rudolph,

thanks for your speedy response. I want to get distance along vertices (the surface) between two vertex points. Is there maybe a matlab function doing this?

Thanks,

Stephan

On Tue, Oct 25, 2011 at 10:54 AM, Rudolph Pienaar < rudolph@nmr.mgh.harvard.edu> wrote:

'mris_pmake' is still very experimental. It's not run as part of the standard recon-all stream, and is more of a post-processing surface tool. It has a somewhat complicated set of dependencies at this stage (among them, a file called 'options.txt' that controls its behavior).

What are you looking to do with it?

Best -=R

On 10/25/11 10:51 , Steph Bickel wrote:

...

Hi,

when trying to use mris_pmake I get error messages: when I run:mris_pmake I get: sh: cannot create lock: Permission denied

mris_pmake I'm sorry, but an error condition has occurred. While I was checking on the options file, I couldn't access the options file. Does it exist?

Exiting to system with code 40

When I run: sudo ./bin/mris_pmake I get: mris_pmake I'm sorry, but an error condition has occurred. While I was processing environment, it seems that the SUBJECTS_DIR env variable is not set.

Exiting to system with code 10

I did specify SUBJECTS_DIR in SetUpFreesurfer.sh that I source in the bashrc file and the variable is set for the other freesurfer functions.

I am using freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0 on ubuntu 11.04.

Any help is much appreciated.

thanks,

Stephan

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

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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

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.mgh.harvard.edu 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.harvard.edu 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.