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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
eazun...@vcu.edu
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