External Email - Use Caution
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 <eazun...@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 $FREESURFER_HOME/bin be
automatically added to the PATH? I tried rebooting, and it still is not
adding it to the PATH. My environment variables appear to be set
correctly because I see this when opening a new terminal. I
also tried modifying the .cshrc file to add the directory to the PATH
manually, but it still will not stick after rebooting.--------
freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 --------Setting up
environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME
/usr/local/freesurfer/7.4.1-1FSFAST_HOME
/usr/local/freesurfer/7.4.1-1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR
/usr/local/freesurfer/7..4.1-1/subjectsMNI_DIR
/usr/local/freesurfer/7.4.1-1/mniFSL_DIR
/usr/local/FSL/fsl_6_0_7_4[cogdmd@cari6
~]$ Thanks,Eddie#############################################################umask
002setenv PATH /usr/local/cuda-9.1/bin:$PATHsetenv 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 Setupsetenv
FSLDIR /usr/local/FSL/fsl_6_0_7_4setenv PATH
${FSLDIR}/share/fsl/bin:${PATH}source ${FSLDIR}/etc/fslconf/fsl.csh#Freesurfer
Setupsetenv FREESURFER_HOME /usr/local/freesurfer/7.4.1-1setenv SUBJECTS_DIR
$FREESURFER_HOME/subjectssource $FREESURFER_HOME/SetUpFreeSurfer.cshalias spm12
'matlab -r "addpath /usr/local/SPM/spm12_r7771/spm12; spm fMRI"'alias conn
'matlab -r "addpath /usr/local/SPM/spm12_r7771/spm12; addpath
/usr/local/SPM/conn; conn"'setenv PATH /home/cogdmd/anaconda3/bin:$PATHsetenv
ANTSPATH /home/cogdmd/ants-2.4.1/binsetenv PATH ${ANTSPATH}:${PATH}setenv PATH
/home/cogdmd/.lcmodel:$PATH############################################################-- Edward
A. ZunigaSenior Research AnalystVirginia Commonwealth UniversityC. Kenneth and
Dianne Wright Center for Clinical and Translational ResearchInstitute for Drug
and Alcohol StudiesCollaborative Advanced Research Imaging (CARI) Facility203
East Cary Street, Suite 202Richmond, Virginia 23219Phone: (804) 828-4184Fax:
(804)
827-2565eazuniga@vcu.edu_______________________________________________Freesurfer
mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
