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".
- You can test using freeview (instructions on wiki); the tksurfer may cause problems, so make sure you test that. At some point, freeview will fully replace tksurfer.
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