External Email - Use Caution
Hello Deanna, Something is executing the “export” command which is fine in bash or sh, but not in csh or tcsh (which needs “setenv”). export: Command not found.You could try manually running the scripts that get sourced with “tcsh -xf” to better see if they return that error, e.g., % tcsh -xf $HOME/.afni/help/all_progs.COMP% tcsh -xf ${FSLDIR}/etc/fslconf/fsl.csh You may want to temporarily rename your .cshrc or comment out the contents before running what’s in $HOME/.cshrc manually. But if something gets run that does an export command, then it won’t matter what is currently set in your environment. - R. On Jul 15, 2022, at 12:48, Deanna Aghbashian <daghbashian07@gmail.com> wrote: External Email - Use Caution Hello FreeSurfer Developers,
I have set up with terminal in tcsh, and it was working without error. However, when I logged on late last week I got an error in setting up environment for FreeSurfer on Mac OS Monterey Version 12.4
-------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSLOUTPUTTYPE=NIFTI_PAIR: Command not found. export: Command not found.. FSL_DIR /usr/local/fsl [MacBook-Pro:~] deanna% nano ~/.cshrc
Within my tcsh profile, I do not have anything to indicate to have FSLOUTPUTTYPE to be NIFTI_PAIR, nor do I have a line to export. I have also checked the SetUpFreeSurfer.csh, FreeSurferEnv.csh. I have tried clearing out my profile and recreating it, deleting and reinstalling FSL and FreeSurfer. When I use echo $FSLOUTPUTTYPE it comes back as NIFTI_GZ. My profile is below: # auto-inserted by @update..afni.binaries : setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace
# set up tab completion for AFNI programs if ( -f $HOME/..afni/help/all_progs.COMP ) then source $HOME/.afni/help/all_progs.COMP endif
if ( $?DYLD_LIBRARY_PATH ) then setenv DYLD_LIBRARY_PATH ${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace else setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace endif set path = ( $path $HOME/abin )
# include directories for FSL setenv FSLDIR /usr/local/fsl source ${FSLDIR}/etc/fslconf/fsl.csh setenv PATH ${FSLDIR}/bin:${PATH}
setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh
Does anyone have any suggestions?
Thanks,
Deanna _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%E2%80%8B%E2%80%...