Dear FreeSurfers,
I am trying to update an mris_pmake command line that works with the pub v5.3.0 version with a new command line that works with pub v6.0.0 version. The purpose is to compute the distance between two vertex points on the pial surface using the cvs_avg35_inMNI152 brain. We are using CentOS (6.6 on the workstation running FS v5.3.0 and 7.4 on the workstation running FS v6.6.0) outside Martinos Center.
nmr-std-env
setenv SUBJECTS_DIR /usr/pubsw/packages/freesurfer/subjects
setenv SUBJECT cvs_avg35_inMNI152
Old command line (gives a reasonable result on v5.3.0):
mris_pmake --subject cvs_avg35_inMNI152_temp --hemi lh --surface0 pial --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:121981,endVertex:132633 Start->End vertices [ 121981->132633 ] Total path cost [ 29.668283 ]
If I try to run this on v6.0.0, I receive the error:
mris_pmake: unrecognized option '--surface0'
I first tried removing --surface0 option, but then the error becomes
mris_pmake: unrecognized option '--curv0'
I then tried removing the --curv0 and eventually --curv 1 options as well, but these gave more similar errors (unrecognized option) or core dumped.
Looking at older posts on the FreeSurfer list, I tried removing all three --surface0 --curv0 --curv 1 options, but this gives a clearly incorrect result where the startVertex and endVertex values are apparently not read from the command line:
Start->End vertices [ 0->0 ] Total path cost [ 0.000000 ]
I tried renaming --surface0 to --surface and --curv0 to --curv, as it seems that some of the options have been renamed, and to some degree this worked as there were no more 'unrecognized option' errors. However, the result is still
Start->End vertices [ 0->0 ] Total path cost [ 0.000000 ]
Any suggestions would be greatly appreciated.
Btw the command line documentation (mris_pmake --help) does not seem to be quite match the version distributed with FS v6.0.0, at least when it comes to the option names for surface and curve, and if there are separate definitions for 0 and 1.
Thank you!
Best regards,
Tommi Raij