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
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