software_setup
====== Differences ====== This shows you the differences between two versions of the page.
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software_setup [2016/08/17 18:29] bdelab |
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. | ||
| + | |||
| + | ====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==== | ====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). | ||
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| <code> | <code> | ||
| cd ~/git | cd ~/git | ||
| - | git clone https://github.com/jyeatman/AFQ.git | + | git clone https://github.com/yeatmanlab/AFQ.git |
| </code> | </code> | ||
| Line 47: | Line 52: | ||
| ====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==== | ||
| Line 70: | Line 73: | ||
| ====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 96: | Line 99: | ||
| ====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 126: | Line 129: | ||
| ====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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| ptb3-matlab | ptb3-matlab | ||
| </code> | </code> | ||
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software_setup.1471458590.txt.gz · Last modified: 2016/08/17 18:29 by bdelab
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