Seminar in diffusion imaging

Monday 4th, 10am-12 in the brain imaging center (BIC).

The BIC needs keycard access - but we will let you in if you don’t have access, please wait at the elevator going down the BIC at 10 for us to come and get you - see: http://practical-neuroimaging.github.io/where_and_when.html#where

Software installation

You will need some software installed on your laptop to follow along.

Please let me (matthew.brett@gmail.com) know if you have any problem with the following instructions. If you come early to the seminar - say 9.30 - then I can help you with your install.

Mac

If you do not have the standard scientific Python packages installed, then we recommend Anaconda to install the packages you need: http://continuum.io/downloads

If you are using Anaconda, you can then do the following from the Terminal.app command prompt:

conda install vtk

Finally you can install the diffusion imaging package (dipy) with:

conda install -c http://nipy.bic.berkeley.edu/scipy_installers/conda dipy

If you do have the standard scientific Python packages already installed, but not through Anaconda, then try:

pip install dipy

from the Terminal.app command prompt.

Windows

If you do not have the standard scientific Python packages installed, then we recommend Anaconda http://continuum.io/downloads

If you are using Anaconda, you should then run this from the Windows cmd prompt:

conda install vtk

If you don’t want to use Anaconda, you could follow the instructions at : http://practical-neuroimaging.github.io/installation.html#if-you-are-using-windows

Either way, you should then run (from the cmd prompt):

pip install -f http://nipy.bic.berkeley.edu/scipy_installers/windows_wheels dipy

Linux

If you are on Linux - you can install the packages you need with something like:

sudo apt-get install python-scipy python-matplotlib python-vtk ipython-notebook python-pip

on Ubuntu or Debian, followed by:

pip install -U ipython[notebook]
pip install dipy