Setup

From Hodaie Lab
Jump to: navigation, search

Start from a fresh Ubuntu 64bit LTS (12.04 at the time of writing) installation.

Update packages to latest. sudo apt-get udpate

Install the following:

Nvidia drivers

sudo add-apt-repository ppa:xorg-edgers/ppa

sudo apt-get update

sudo apt-get install nvidia-current

Data sharing and encryption

Dropbox
Truecrypt
CAUTION - Truecrypt has suspeciously stopped development, ALL VERSIONS AFTER 17.1a IS CONSIDERED COMPROMISED. DOWNLOAD ONLY FROM TRUSTED SOURCES. DO NOT DOWNLOAD THE VERSION FROM http://truecrypt.sourceforge.net/.


Setup NeuroDebian Repository

wget -O- http://neuro.debian.net/lists/precise.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list

sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9

sudo apt-get update

Install FSL

sudo apt-get install fsl

Add the following into ~/.bashrc
Change paths as needed.

############### MY CONFIGS ###############
alias grep='grep --color=auto -i'
alias subjd='setenv SUBJECTS_DIR `pwd`'
alias ls='ls --group-directories-first --color=auto'
alias pwdc='pwd | tr "\n" " " | xsel -bi'

export APP_PATH=/home/apps
export HLAB_SCRIPT_PATH=${APP_PATH}/scripts/fsScripts
export SLICER4_HOME=/home/apps/Slicer-4.3.1-linux-amd64
export ANTSPATH=/usr/lib/ants/
export PATH=${PATH}:${HLAB_SCRIPT_PATH}:${HLAB_SCRIPT_PATH}/motion_correction:${APP_PATH}/mricron:/usr/local/cuda-5.5/bin
export PATH=${PATH}:${APP_PATH}/mrtrix:$ANTSPATH
export FREESURFER_HOME=${APP_PATH}/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export NRRD_STATE_KEYVALUEPAIRS_PROPAGATE=1

source /etc/fsl/5.0/fsl.sh


If run into apt-error such as

The following packages have unmet dependencies:
 freeglut3-dev : Depends: libgl1-mesa-dev or
                          libgl-dev
                 Depends: libglu1-mesa-dev but it is not going to be installed or
                          libglu-dev
E: Unable to correct problems, you have held broken packages.

Then try to run this [1][2]

sudo apt-get install -V libglapi-mesa-lts-raring libgl1-mesa-glx-lts-raring xserver-xorg-lts-raring xserver-xorg-input-all-lts-raring xserver-xorg-video-all-lts-raring libgl1-mesa-dri-lts-raring x11-xserver-utils-lts-raring libglapi-mesa-lts-raring:i386 libgl1-mesa-dri-lts-raring:i386 libgl1-mesa-glx-lts-raring:i386

Install CUPS drivers for Google cloud print

source:http://askubuntu.com/questions/158874/how-can-i-easily-set-up-a-google-cloud-print-printer

To install it and configure it:

sudo add-apt-repository ppa:simon-cadman/cups-cloud-print
sudo apt-get update
sudo apt-get install cupscloudprint
sudo /usr/share/cloudprint-cups/setupcloudprint.py

After it asks for Google Credentials ( it will only do this is the first time you have used CUPS CloudPrint, or your credentials are invalid ) it will then ask if you wish to add all printers from your Google Account.

To make it work with Google's 2 Step Verification system, you must create a "Device Specific" password, to do this go to:Google.com>Log in with your account>Click on your user name>Security>Edit authorizing applications>Enter your account pasword>set the password.

If you say ‘Y’ here, it will add all printers that are currently not added to your CUPS install.

If you would prefer to add the printers manually, say ‘N’ here, and add a printer manually:

Add a new printer ( via http://127.0.0.1:631 or usual interface ) as a ‘Google Cloud Print’ network printer. Select the ‘Make’ as Google, and ‘Model’ as Cloud Print.

/usr/lib/cloudprint-cups/listcloudprinters.py

Python library setup

Install pip if not already:

sudo apt-get install python-pip
sudo apt-get install python-vtk
#upgrade distribute to newest
sudo easy_install -U distribute

Install necessary libraries:

sudo pip install cython scipy numpy matplotlib ipython pandas nibabel dipy