External Email - Use Caution Dear Rudolph, Thank you for following up. I changed flags and tried it again with this command line:
mris_pmake --subject cvs_avg35_inMNI152_temp --hemi lh --surfaceFile pial --curvatureFile sulc --mpmOverlayArgs euclidean --mpmProgID pathFind --mpmArgs startVertex:121981,endVertex:132633 There seems to be a similar problem with the flag since message is the same: mris_pmake: unrecognized option `—surfaceFile' Any further ideas? Thank you for your help! Best > Am 30.07.2019 um 16:53 schrieb Rudolph Pienaar <rudo...@nmr.mgh.harvard.edu>: > > > Apology if this is a repeat email. I used the wrong email address in my > reply. I was one of the original > authors of `mris_pmake` although it's been (quite) a few years now. I > do remember that at some point the CLI changed, and given the FS > release cycle it took a while for this to make it into production. > > Anyway, yes, the flags changed and looks like the documentation didn't. > I looked at the code and sort of (rustily) remembered where things > changed. Try using the flags below instead. You should be able to > figure out the mapping I think. So what used to be '--surface0' is now > '--surfaceFile'. Similary, the old '--surface1' is now ' > --secondarySurfaceFile', etc. > > Please try with these new flags where appropriate and let us know if it > works. It would also be useful if you posted your full CLI when you try > and run a command. > > Best > > > > startVertex > endVertex > surfaceFile > secondarySurfaceFile > curvatureFile > secondaryCurvature > patchFile > labelFile > labelFileAuxSurface > costFile > b_labelFile_save > b_patchFile_save > b_transitionPenalties > b_useAbsCurvs > controlPort > timeoutSec > b_syslogPrepend > userMessages > sysMessages > resultMessages > stdout > costCurvFile > b_mpmProgUse > b_mpmOverlayUse > mpmProgID > mpmArgs > mpmOverlayArgs > b_exitOnDone > b_costPathSave > mpmOverlayID > > >> On Mon, 2019-07-29 at 21:36 +0200, Sebastian Strauss wrote: >> External Email - Use Caution >> >> Dear Freesurfers, >> >> I am trying to calculate distances using mris_pmake with Freesurfer >> Version 6.0.0. When using the command line the following error >> appears: >> mris_pmake: unrecognized option '—surface0' >> >> In January the similar question ( >> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg60835.html >> ) was ask but without any answers. Does anyone have the same problem >> btw any suggestions? >> >> Thank you! >> >> Best wishes >> >> Sebastian >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
