so your path must be wrong then. Are you sourcing $FREESURFER_HOME/FreeSurferEnv.csh? That is, in your .login or .cshrc or whatever gets run at startup do you do:
source $FREESURFER_HOME/FreeSurferEnv.csh try running that at the command line and see if it finds mris_preproc afterwards. cheers Bruce On Tue, 5 Jun 2012, Richter, Julia wrote: > nothing happens when typing "which mris_prepoc", command not found when > typing only "mris_preproc" > ________________________________________ > Von: Bruce Fischl [fis...@nmr.mgh.harvard.edu] > Gesendet: Dienstag, 5. Juni 2012 15:25 > Bis: Richter, Julia > Cc: freesurfer@nmr.mgh.harvard.edu > Betreff: Re: AW: [Freesurfer] mris_preproc > > okay, how about: > > which mris_preproc > > and just > > mris_preproc > > On Tue, 5 Jun 2012, Richter, Julia wrote: > >> after typing your command in my terminal window, it appears: >> >> /usr/local/freesurfer/bin/mris_preproc >> ________________________________________ >> Von: Bruce Fischl [fis...@nmr.mgh.harvard.edu] >> Gesendet: Dienstag, 5. Juni 2012 15:05 >> Bis: Richter, Julia >> Cc: freesurfer@nmr.mgh.harvard.edu >> Betreff: Re: [Freesurfer] mris_preproc >> >> Hi Julia >> >> that seems unlikely. What happens when you type: >> >> ls $FREESURFER_HOME/bin/mris_preproc >> >> cheers >> Bruce >> On Tue, 5 Jun 2012, >> Richter, Julia wrote: >> >>> Could it be that the mris_preproc and the mri_glmfit file are missing in my >>> freesurfer package? If so, can anybody send them to me? >>> >>> Thank you very much, >>> >>> Julia >>> ________________________________ >>> Von: Richter, Julia >>> Gesendet: Dienstag, 5. Juni 2012 10:11 >>> Bis: freesurfer@nmr.mgh.harvard.edu >>> Betreff: mris_preproc >>> >>> Dear FreeSurfer experts, >>> >>> I am trying to run mris_preproc after caching my data. As command lines, I >>> am typing: >>> >>> mris_preproc --fsgd file.fsgd \ >>> --cache-in thickness.fwhm10.fsaverage \ >>> --target fsaverage --hemi lh \ >>> --out lh.allpatients.thickness10.mgh >>> >>> Everytime I am trying to run these commands, it tells me that it does not >>> know the command mris_preproc. I have no clue what is going on here. Any >>> suggestions? >>> >>> Thanks for your help, >>> >>> best >>> Julia >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> >> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
