Here's how to install Neuroimaging Software on Linux, WSL2 and macOS.

This script installs a large number of NeuroImaging related software on Linux (I prefer Linux Mint 21.1, but Ubuntu 22.04 also works). It is not maintained anymore to install on Windows-WSL2 (latest Win11 preferably) or macOS. Results may vary...

It is assumed you have an nvidia gpu.

Which NeuroImaging software

The script installs the latest stable versions of:

• Anaconda3
• Video Studio Code
• nvidia cuda
• mrtrix3
• FSL
• Docker
• Freesurfer
• ANTs
• dcm2niix
• dcm2bids
• DCMTK
• GDCM
• SPM12
• cat12
• lead-DBS
• conn toolbox
• KUL_NeuroImaging_tools
• KUL_VBG
• KUL_FWT
• Mevislab
• Scilpy (in the conda environment "scilpy")
• FastSurfer (in the conda environment "fastsurfer_gpu")
• Karawun (in the conda environment "KarawunEnv")

Output of a terminal after installation

The terminal in WSL2, macOS and Linux will show which version of software is currently installed.

Prerequisites

All (but optional)

• Matlab (R2017b or later) - only needed if you use spm12, conn, cat12, lead-dbs

Linux

• Should run out of the box.
• follow the instructions given by the installer

Windows with WSL2

• Install win11, perform all updates
• Install nvidia-cuda: follow https://docs.microsoft.com/en-us/windows/ai/directml/gpu-cuda-in-wsl
• Open powershell as administrator and exe: wsl --install
• reboot when asked
• after reboot you will be asked to setup the user/passwd
• INSIDE WIN11: install
  • visual studio code
  • docker desktop & setup the ubuntu as wsl integration
• open Ubuntu in wsl2
• follow the instructions given by the installer

macOS

• Should work out of the box
• follow the instructions given by the installer

Installation notes

Open a terminal. Copy the following commands into terminal.

wget https://raw.githubusercontent.com/treanus/KUL_Linux_Installation/master/KUL_Install_NeuroImagingSoftware.sh

chmod +x KUL_Install_NeuroImagingSoftware.sh

Now run the script

./KUL_Install_NeuroImagingSoftware.sh

In a first step this will install Anaconda3. Follow the installation instruction, and accept the license and initialization. Reboot when asked.

Rerun the script.

./KUL_Install_NeuroImagingSoftware.sh

Depending on the cpu and the internet connection speed this will take a few hours.

On some occasions you will be asked to enter your password and/or to confirm the installation.

Post-Install

• The freesurfer license file needs to be installed. Put it in $KUL_apps_DIR/freesurfer_license
• Start matlab, add spm12 and conn to the path. The path for spm12 and conn is $HOME/KUL_apps/spm and conn.
• On macOS open Docker Desktop; in Resources/FileSharing add the folder with the freesurfer license.