heffjos / new_install_config

keeps track of installation procedure for new ubuntu (16.04 and 18.04) installtions

new_install_config

keeps track of installation procedure for new ubuntu (20.04) installtions

Ethernet (if needed)

1. Request ethernet port activation for either managed or collaborative network. Linux machines not set with a static ip address will have network access whereas ones not with a static ip address will not.
2. If needed, request a static ip address from help. This is primarily done for machines on unmanaged network.
3. Request machine added to DNS from G.
4. Configure the static ip address on the machine. This is done with a file in /etc/netplan.
5. Request RCC access from M.

Upgrade packages

At terminal run:

1. apt-get update
2. apt-get upgrade
3. apt-get install vim

Additional repositories

Neurodebian

There are instructions how to do this on the neurodebian website.

Chrome web browser

Use the .deb file provided by google: https://www.google.com/chrome

1. wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb
2. sudo dpkg -i google-chrome-stable_current_amd64.deb
3. The .deb file will add the official Google repository to the system. Check /etc/apt/sources.list.d/google-chrome.list

Docker

Follow this website: https://docs.docker.com/engine/install/ubuntu/

R

• Follow this website: https://cran.r-project.org/bin/linux/ubuntu/fullREADME.html
• Install the c2d4u ppa. This makes installing r packages so much easier.

Afni

Follow the installation instructions: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_ubuntu20.html

• Use option -bindir ABIN to set AFNI binary directory to ABIN
• mkdir ${ABIN}/system_config and the system afnirc file to this directory
• copy/create afnirc to ${ABIN}/system_config
• add export AFNI_SYSTEM_AFNIRC=/opt/afni/system_config/afnirc to /etc/bash.bashrc
  • The config sets the path for the atlases and plugins. These are needed for afni to load them.

FSL

Follow the installation instructions: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Linux

• Set the correct installation location. FSL creates symbolic links for some binaries so they will not be updated if the FSL folder is moved.

ANTS

Use guide to build it from source: https://github.com/ANTsX/ANTs/wiki/Compiling-ANTs-on-Linux-and-Mac-OS

• Install ccmake with sudo apt-get install cmake-curses-gui

Freesurfer

Install instructions are on this website: https://surfer.nmr.mgh.harvard.edu/fswiki//FS7_linux

Workbench

Download from this website: https://www.humanconnectome.org/software/get-connectome-workbench