Hi Freesurfer experts,

I am new to freesurfer. I installed the last freesurfer version (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) and I am trying to compute the shortest cortical path between two sets of vertices.

1- Using the command mris_pmake updated

If I understand correctly according to

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027543.html

mris_pmake has been updated, but the command

mris_pmake --subj bert --hemi lh --surface smoothwm --mpmProg autodijk --mpmArgs vertexPolar:0 --mpmOverlay euclidean

throws the following error

#####################"

mris_pmake: option '--surface' is ambiguous; possibilities: '--surface0' '--surface1'

#####################"

Following the complain, I tried

mris_pmake --subject bert --hemi lh --surface0 smoothwm --surface1 smoothwm --mpmProg autodijk --mpmArgs vertexPolar:11 --mpmOverlay euclidean

This seems to work and produces options.txt and user_msg.log files in the current directory. However I am unable to find the output

lh.autodijk.crv

and that's where the path lengths are stored, right ?

2- making dsh work:

I get the following error when trying to run dsh

Traceback (most recent call last):
File "/usr/local/freesurfer/bin/dsh", line 16, in <module>
from dgmsocket import *
ImportError: No module named dgmsocket

So I commented this import as well the line "G_socket = C_dgmsocket(Gstr_host, string.atoi(Gstr_port))".

Now dsh seems working in the begining but then I have the following

#################################################

sh: 1: SSocket_client: not found
46.860310
Engine successfully started and environment parsed.
Ready for user input. Type 'HELP' for help.
1 > Start->End vertices                                       [ 11->6398 ]
Total path cost                                          [ 46.860310 ]
process died.
/usr/local/freesurfer/bin/dsh

   Sorry, but some error occurred.
   While attempting dijkstra_spawn(),
   the process died unexpectedly

Exiting to system with code 10.

###########################################

Any help is appreciated !

Thanks.

Salma