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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 $FREESURFER_HOME/bin be automatically added to the PATH? I tried rebooting, and it still is not adding it to the PATH. My environment variables appear to be set correctly because I see this when opening a new terminal. I also tried modifying the .cshrc file to add the directory to the PATH manually, but it still will not stick after rebooting.-------- freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /usr/local/freesurfer/7.4.1-1FSFAST_HOME /usr/local/freesurfer/7.4.1-1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /usr/local/freesurfer/7..4.1-1/subjectsMNI_DIR /usr/local/freesurfer/7.4.1-1/mniFSL_DIR /usr/local/FSL/fsl_6_0_7_4[cogdmd@cari6 ~]$ 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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%E2%80%8B
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Moving the two lines to the end of the init file and removing the SUBJECTS_DIR line resolved the issue.
Thank you so much!
Eddie
On Mon, Oct 9, 2023 at 4:45 PM fsbuild fsbuild@contbay.com wrote:
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 CautionHello,
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1EPqQFBq1vsw25Wvmdr-HsdKTC6fwINyDhdSCN4ecnGMr4F...
freesurfer@nmr.mgh.harvard.edu
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Edward Zuniga -
fsbuild