External Email - Use Caution
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 <fsbu...@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 <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
> $FREESURFER_HOME/bin be automatically added to the PATH? I tried rebooting,
> and it still is not adding it to the PATH. My environment variables appear
> to be set correctly because I see this when opening a new terminal. I
> also tried modifying the .cshrc file to add the directory to the PATH
> manually, but it still will not stick after rebooting.
>
> -------- freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 --------
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME /usr/local/freesurfer/7.4.1-1
> FSFAST_HOME /usr/local/freesurfer/7.4.1-1/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR /usr/local/freesurfer/7.4.1-1/subjects
> MNI_DIR /usr/local/freesurfer/7.4.1-1/mni
> FSL_DIR /usr/local/FSL/fsl_6_0_7_4
> [cogdmd@cari6 ~]$
>
> 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
> _______________________________________________
> Freesurfer mailing list
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>
>
>
--
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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