software_setup
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software_setup [2016/08/17 18:28] bdelab created |
software_setup [2016/08/17 18:29] bdelab |
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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. | ||
| - | ==Setting up a user account== | + | ====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 11: | ||
| 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> | ||
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| 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 | ||
| Line 33: | Line 33: | ||
| </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> | ||
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| </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. 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: | ||
| <code> | <code> | ||
| Line 52: | Line 52: | ||
| </code> | </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 59: | ||
| </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> | ||
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| </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> | ||
| Line 77: | Line 77: | ||
| </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> | ||
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| </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> | ||
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| </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> | ||
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| - | ==Psychtoolbox for Matlab== | + | ====Psychtoolbox for Matlab==== |
| Requires Neurodebian repo to install. | Requires Neurodebian repo to install. | ||
| <code> | <code> | ||
software_setup.txt · Last modified: 2019/05/15 23:14 by thclark
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