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.ht...
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