If you add these 2 commands to setup the freesurfer environment, e.g., for csh/tcsh as your default shell,

$ setenv FREESURFER_HOME /usr/local/freesurfer/7.4.1-1

$ source $FREESURFER_HOME/SetUpFreeSurfer.csh

- to your shell initialization file, $HOME/.cshrc, then FREESURFER_HOME, SUBJECTS_DIR, PATH, etc., should automatically set/modified by source'ing SetUpFreeSurfer.csh when you open a new terminal window.   There is no need to subsequently set SUBJECTS_DIR or other freesurfer environment variables in your shell init file (or in the current terminal window session) unless the settings should be different than the defaults.  Most people add those 2 commands to be the last 2 lines in their shell init file.

I would check the defaults set in the current shell environment using only those 2 commands above in your shell init file after opening a new terminal window,

$ env | sort

… and check FREESURFER_HOME, SUBJECTS_DIR, PATH are set …

The freeview command should already be found in your path, i.e., you should see …

$ which freeview

/usr/local/freesurfer/7.4.1-1/bin/freeview

- R.

On Oct 9, 2023, at 14:56, Edward Zuniga <eazuniga@vcu.edu> wrote:

        External Email - Use Caution        

Hello,

I am attempting to install FreeSurfer on a Centos 7 workstation using the tcsh shell.. Below are the contents of my .cshrc file. Should $FREESURFER_HOME/bin be automatically added to the PATH? I tried rebooting, and it still is not adding it to the PATH. My environment variables appear to be set correctly  because I see this when opening a new terminal. I also tried modifying the .cshrc file to add the directory to the PATH manually, but it still will not stick after rebooting.

-------- freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer/7.4.1-1
FSFAST_HOME       /usr/local/freesurfer/7.4.1-1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/7.4.1-1/subjects
MNI_DIR           /usr/local/freesurfer/7.4.1-1/mni
FSL_DIR           /usr/local/FSL/fsl_6_0_7_4
[cogdmd@cari6 ~]$ 

Thanks,

Eddie

#############################################################

umask 002

setenv PATH /usr/local/cuda-9.1/bin:$PATH
setenv LD_LIBRARY_PATH /usr/local/cuda-9.1/lib64

# auto-inserted by @update.afni.binaries :
set path = ( $path  /home/cogdmd/abin  ) 
setenv R_LIBS ~/R

#FSL Setup
setenv FSLDIR /usr/local/FSL/fsl_6_0_7_4
setenv PATH ${FSLDIR}/share/fsl/bin:${PATH}
source ${FSLDIR}/etc/fslconf/fsl.csh

#Freesurfer Setup
setenv FREESURFER_HOME /usr/local/freesurfer/7.4.1-1
setenv SUBJECTS_DIR $FREESURFER_HOME/subjects
source $FREESURFER_HOME/SetUpFreeSurfer.csh

alias spm12 'matlab -r "addpath /usr/local/SPM/spm12_r7771/spm12; spm fMRI"'
alias conn 'matlab -r "addpath /usr/local/SPM/spm12_r7771/spm12; addpath /usr/local/SPM/conn; conn"'

setenv PATH /home/cogdmd/anaconda3/bin:$PATH

setenv ANTSPATH /home/cogdmd/ants-2.4.1/bin
setenv PATH ${ANTSPATH}:${PATH}

setenv PATH /home/cogdmd/.lcmodel:$PATH

############################################################

-- 

Edward A. Zuniga
Senior Research Analyst

Virginia Commonwealth University
C. Kenneth and Dianne Wright Center for Clinical and Translational Research

Institute for Drug and Alcohol Studies

Collaborative Advanced Research Imaging (CARI) Facility
203 East Cary Street, Suite 202
Richmond, Virginia 23219
Phone: (804) 828-4184
Fax: (804) 827-2565
eazuniga@vcu.edu

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