Re: [Freesurfer] mris_pmake issue
OK -- looked again -- and I need to fix the in-line help obviously. Anyway, this works: mris_pmake --subjecttestSubject \ --hemi lh \ --surfacepial\ --curv sulc\ --mpmOverlay euclidean \ --mpmProgpathFind\ --mpmArgsvertexStart:121981,vertexEnd:132633 (obviously use your ) Try that and let me know. Best On Tue, 2019-07-30 at 17:33 +0200, Sebastian Strauss wrote: > 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
Re: [Freesurfer] mris_pmake issue
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 : > > > 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
Re: [Freesurfer] mris_pmake issue
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] mris_pmake issue
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
