Difference between revisions of "Software Setup"
From Brain Development & Education Lab Wiki
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| − | We rely on a number of different software packages to analyze MRI and MEG data. Here is a growing tally of what we use and where to get it. Most of these tools reside on github and you should definitely use git to clone the repositories rather than download a snapshot of the code. | + | We rely on a number of different software packages to analyze MRI and MEG data. Here is a growing tally of what we use and where to get it. Most of these tools reside on github and you should definitely use git to clone the repositories rather than download a snapshot of the code. |
| − | + | ||
==Yeatman Lab Tools== | ==Yeatman Lab Tools== | ||
git clone https://github.com/yeatmanlab/BrainTools.git | git clone https://github.com/yeatmanlab/BrainTools.git | ||
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Python based toolbox for dealing with nifti images. While nibabel is on github we suggest installing using pip: | Python based toolbox for dealing with nifti images. While nibabel is on github we suggest installing using pip: | ||
pip install nibabel | pip install nibabel | ||
| + | ==Neurodebian repo== | ||
| + | wget -O- http://neuro.debian.net/lists/trusty.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list | ||
| + | sudo apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 0xA5D32F012649A5A9 | ||
Revision as of 22:36, 2 March 2016
We rely on a number of different software packages to analyze MRI and MEG data. Here is a growing tally of what we use and where to get it. Most of these tools reside on github and you should definitely use git to clone the repositories rather than download a snapshot of the code.
Contents
Yeatman Lab Tools
git clone https://github.com/yeatmanlab/BrainTools.git
Vistasoft
MATLAB based toolbox, from Brian Wandell's lab at Stanford, that contains many functions we rely on for analyzing diffusion MRI and functional MRI data
git clone https://github.com/vistalab/vistasoft.git
Automated Fiber Quantification
git clone https://github.com/jyeatman/AFQ.git
Anaconda
Each user should have anaconda set up to manage their Python packages. See instructions here:
https://www.continuum.io/downloads
nibabel
Python based toolbox for dealing with nifti images. While nibabel is on github we suggest installing using pip:
pip install nibabel
Neurodebian repo
wget -O- http://neuro.debian.net/lists/trusty.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list sudo apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 0xA5D32F012649A5A9
