Setting the Environment Variables and File Permissions

Setting the voxelDesk Environment

In order to run voxelDesk from the command line, the following lines should be added to your bash_profile (or equivalent) file:

export VXD_HOME=<path to vxdHome folder>
export PATH=${VXD_HOME}:${PATH}

where the vxdHome is the folder into which the VoxelDesk source files have been copied.

Once the bash_profile (or equivalent) file has been modified, either open a new terminal window to apply the changes, or type:

source ~/.bash_profile

in the existing terminal window.

It is worth checking at this point that the FSL environment variables have also been set up (the FSL installer should have taken care of this). Check that the folllowing lines, or something similar, are present in your bash_profile (or equivalent) file:

FSLDIR=/usr/local/fsl
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH
. ${FSLDIR}/etc/fslconf/fsl.sh

Setting File Permissions

Navigate to the VXD_HOME folder:

cd $VXD_HOME

The python files in this parent folder are the core voxelDesk command-line functions. These need to be given execute permission, using the following command:

chmod +x *.py

Once the above steps are complete, the command-line functions can be executed from any location.

Verifying the Installation

You can verify the installation and setup have been successful by opening a terminal window, and running:

vxdSort.py --help

This should display the guidance for running vxdSort in the terminal window.

Note

If the above does not work, make sure the vxd conda environment is active (you should see (vxd) at the command prompt). If it isn’t, type:

conda activate vxd

The vxd conda environment should always be activated before running voxelDesk commands.