software_setup
====== Differences ====== This shows you the differences between two versions of the page.
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software_setup [2016/08/17 18:28] bdelab created |
software_setup [2019/05/15 23:14] (current) thclark [Psychtoolbox for Matlab] |
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| + | ====== Software Setup ====== | ||
| 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. | ||
| - | ==Setting up a user account== | + | |
| + | ====I-LABS IT Ticket==== | ||
| + | If you need to submit an IT ticket, do so at [[http://help.ilabs.uw.edu/otrs/customer.pl]]. For help getting an account on this site, contact [[dubinc@uw.edu|Cary Dubinksy]]. | ||
| + | |||
| + | ====Setting up a user account==== | ||
| To add a new user with sudo privileges (userid should be maintained across all systems). | To add a new user with sudo privileges (userid should be maintained across all systems). | ||
| <code> | <code> | ||
| Line 11: | Line 16: | ||
| Have new user enter desired password. | Have new user enter desired password. | ||
| - | ==Git== | + | ====Git==== |
| All git directories should be maintained together. | All git directories should be maintained together. | ||
| <code> | <code> | ||
| mkdir ~/git | mkdir ~/git | ||
| </code> | </code> | ||
| - | ==Yeatman Lab Tools== | + | ====Yeatman Lab Tools==== |
| <code> | <code> | ||
| cd ~/git | cd ~/git | ||
| git clone https://github.com/yeatmanlab/BrainTools.git | git clone https://github.com/yeatmanlab/BrainTools.git | ||
| </code> | </code> | ||
| - | ==Vistasoft== | + | ====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 | 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 | ||
| <code> | <code> | ||
| Line 27: | Line 32: | ||
| git clone https://github.com/vistalab/vistasoft.git | git clone https://github.com/vistalab/vistasoft.git | ||
| </code> | </code> | ||
| - | ==Automated Fiber Quantification== | + | ====Automated Fiber Quantification==== |
| <code> | <code> | ||
| cd ~/git | cd ~/git | ||
| - | git clone https://github.com/jyeatman/AFQ.git | + | git clone https://github.com/yeatmanlab/AFQ.git |
| </code> | </code> | ||
| - | ==Setting up Matlab for AFQ== | + | ====Setting up Matlab for AFQ==== |
| AFQ requires Matlab r2014a, SPM8, Vistasoft, and AFQ. If you wish to use a different version of Matlab for your core coding, you can set aliases in your ~/.bashrc file | AFQ requires Matlab r2014a, SPM8, Vistasoft, and AFQ. If you wish to use a different version of Matlab for your core coding, you can set aliases in your ~/.bashrc file | ||
| <code> | <code> | ||
| Line 46: | Line 51: | ||
| </code> | </code> | ||
| - | ==Anaconda== | + | ====Anaconda==== |
| - | Each user should have anaconda set up to manage their Python packages. Do this before installing nibabel and dipy. Anaconda will manage versions and dependencies for each user separately. Each install will be specific to the user that installs it. Do not install as root, as you will deny yourself privileges to your own directory. You must restart your terminal session after install before using Python or the conda command. See instructions here: | + | Each user should have anaconda set up to manage their Python packages. **All code for REDCap was written using Python3.** Do this before installing nibabel and dipy. Anaconda will manage versions and dependencies for each user separately. Each install will be specific to the user that installs it. Do not install as root, as you will deny yourself privileges to your own directory. You must restart your terminal session after install before using Python or the conda command. See instructions here: https://www.continuum.io/downloads |
| - | <code> | + | |
| - | https://www.continuum.io/downloads | + | |
| - | </code> | + | |
| - | ==nibabel and DIPY== | + | ====nibabel and DIPY==== |
| 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: | ||
| <code> | <code> | ||
| Line 59: | Line 62: | ||
| </code> | </code> | ||
| - | ==pyAFQ== | + | ====pyAFQ==== |
| While we are still in the processing of developing a full implementation of AFQ in Python, some of these files are required for running DKI. | While we are still in the processing of developing a full implementation of AFQ in Python, some of these files are required for running DKI. | ||
| <code> | <code> | ||
| Line 69: | Line 72: | ||
| </code> | </code> | ||
| - | ==Neurodebian repo== | + | ====Neurodebian repo==== |
| - | The [http://neuro.debian.net/ neurodebian project] is an incredible resource making it easy to install most of the widely used nueroimaging software packages. | + | The [[http://neuro.debian.net/|neurodebian project]] is an incredible resource making it easy to install most of the widely used nueroimaging software packages. |
| <code> | <code> | ||
| wget -O- http://neuro.debian.net/lists/trusty.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list | wget -O- http://neuro.debian.net/lists/trusty.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list | ||
| Line 77: | Line 80: | ||
| </code> | </code> | ||
| - | ==FSL, ANTS and other Neurodebian packages== | + | ====FSL, ANTS and other Neurodebian packages==== |
| Once you have added the neurodebian repos you can easily install fsl and other packages | Once you have added the neurodebian repos you can easily install fsl and other packages | ||
| <code> | <code> | ||
| Line 95: | Line 98: | ||
| </code> | </code> | ||
| - | ==Freesurfer== | + | ====Freesurfer==== |
| - | The steps and download is [https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall here], instructions are repeated below. Download the Linux CentOS 6 x86_64 install file. | + | The steps and download is [[https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall|here]], instructions are repeated below. Download the Linux CentOS 6 x86_64 install file. |
| <code> | <code> | ||
| cd ~/Downloads | cd ~/Downloads | ||
| - | sudo tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz | + | sudo tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz |
| </code> | </code> | ||
| - | You'll need to register [https://surfer.nmr.mgh.harvard.edu/registration.html here]. The registration e-mail will tell you which text to copy into a new file, which you can create/edit by | + | You'll need to register [[https://surfer.nmr.mgh.harvard.edu/registration.html|here]]. The registration e-mail will tell you which text to copy into a new file, which you can create/edit by |
| <code> | <code> | ||
| sudo gedit /usr/local/freesurfer/license.txt | sudo gedit /usr/local/freesurfer/license.txt | ||
| Line 125: | Line 128: | ||
| </code> | </code> | ||
| - | ==SPM8== | + | ====SPM8==== |
| - | Fill out the form located [http://www.fil.ion.ucl.ac.uk/spm/software/download/ here] in order, making sure to select SPM8. Run this script from the terminal to install. | + | Fill out the form located [[http://www.fil.ion.ucl.ac.uk/spm/software/download/|here]] in order, making sure to select SPM8. Run this script from the terminal to install. |
| <code> | <code> | ||
| unzip ~/Downloads/spm8.zip -d ~/Documents/MATLAB/ | unzip ~/Downloads/spm8.zip -d ~/Documents/MATLAB/ | ||
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| - | ==Psychtoolbox for Matlab== | + | ====Psychtoolbox for Matlab==== |
| Requires Neurodebian repo to install. | Requires Neurodebian repo to install. | ||
| <code> | <code> | ||
| Line 141: | Line 144: | ||
| ptb3-matlab | ptb3-matlab | ||
| </code> | </code> | ||
| + | |||
software_setup.1471458494.txt.gz · Last modified: 2016/08/17 18:28 by bdelab
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