Neuro Software

Download software Download the linux software version. Run the following command: sudo tar -C /usr/local -xzvf /mnt/c/Users/*[your_username]*/Downloads/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz You will also need to install some dependancies: sudo apt-get install tcsh sudo apt-get install libglu1 sudo apt-get install libxss1 Post-Install Configurations Add Freesurfer to your path:

Get the latest ANTs code Download the latest code into an arbitrary directory, I use ~/code: mkdir ~/code cd ~/code git clone https://github.com/ANTsX/ANTs.git You will also need to install the ZLIB libraries:

Download NiftyReg Obtain the newest version of NiftyReg or by running the following: mkdir -p ~/code/niftyreg_source cd ~/code/niftyreg_source git clone https://github.com/SuperElastix/niftyreg.git Run CMake/Make Make the build and install directories.

Installing on Pop_OS! You will first need to run the following steps prior to installing FSL. The following steps were originally written here here . Make sure you run a backup prior to performing this hack… just in case.

Download ART Download the newest version of ART Make a new directory for the install and extract the tar package into it: mkdir ~/Applications/ART cd ~/Applications/ART tar -xvzf /mnt/c/Users/*[your_username]*/Downloads/acpcdetect2.0*.tar.gz Post Configuration Set the ARTHOME environment variable and add the binary directory to your PATH by editing your ~/.

Install Make Install build essentials and Make first: sudo apt-get install make sudo apt-get update && sudo apt-get install build-essential Install CMake Download the latest version of the CMake executable.

Run Install Run the following code in a linux terminal: sudo apt-get install dcm2niix Install Dependencies There are a few packages that allow dcm2niix to run faster: sudo apt-get install python-gdcm sudo apt-get install pigz