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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:

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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

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