Installation based on wiki instructions

Make sure the VM has been customized, especially setting the shell to tcsh, and changing the /usr/local permissions.

• Download and copy installation file to /usr/local
• Unpack: open a terminal, nagivation to /usr/local, tar xzvf freesurfer....
• Copy the .license file to the /usr/local/freesurfer directory
• Edit the .tcshrc file to add the environment variables, including pointing SUBJECTS_DIR to LinuxShare, so your file might look like this:

setenv FSLDIR /usr/local/fsl
source ${FSLDIR}/etc/fslconf/fsl.csh
setenv PATH ${FSLDIR}/bin:$PATH

setenv FSL_DIR $FSLDIR
setenv FREESURFER_HOME /usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
setenv SUBJECTS_DIR /mnt/hgfs/LinuxShare/subjects4freesurfer

Note that "FSL_DIR" is a FreeSurfer variable, which is why it is not duplicate the the FSL "FSLDIR".

...

Image Added

Ubuntu

Hello,

This is a known when running freesurfer on Ubuntu systems. The solution is
addressed in the FAQ section on the frresurfer download page:

  https://surfer.nmr.mgh.harvard.edu/fswiki/Download

pecifically, the solution is to go into you system's lib directory and
create a symlink as follows:

  $> cd /usr/lib/x86_64 (or something similar depending upon exact version)
  $> sudo ln -s libjpeg.so.8 libjpeg.so.62
  $> sudo ln -s libtiff.so.4 libtiff.so.3

This should solve it. Best,

-Zeke