This requires Vagrant & VirtualBox. Trust me, it's gonna be great.
- get freesurfer & mne packages (see below)
- copy them to
provision/folder - run
vagrant up - go get a coffee, maybe lunch
- see
provision/jupyter-lab.txtfor URL to open
What do it do though?
- sets up / compiles FSL, FreeSurfer, MNE, OpenMEEG, MRtrix3
- & Python 3.6 w/ all required packages
- starts a Jupyter Notebook & Lab instance to interact with software
The software is all available
- freesurfer -> bem/headmat, dmr/trac, decim surf, ct/elec
- subparc & trac -> conn
- conn & dceim surf & headmat -> eeg/meg/bold fwd
- & ct/elec -> seeg fwd
For academic reasons, these softwares require registration to get them. Place
the packages in the provision/ subdirectory.
If you have access to our cluster, you should be able to copy them from the
/soft/dl/ folder, but you still need to get a FreeSurfer license.
First, download FreeSurfer v6 for Linux
ftp:https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
This can take a while as FreeSurfer is a large download.
While it's downloading, you should complete registration at
https://surfer.nmr.mgh.harvard.edu/fswiki/Registration
(which is free), and they will send you a small license file with some text like
[email protected]
123456
*jf0a0fj2932j
jsrl900r9u309
which you should place in a text file at provision/freesurfer-license.txt.
MNE tools are yet another package which requires manual registration and download from
http:https://www.nmr.mgh.harvard.edu/martinos/userInfo/data/MNE_register/index.php
After registration, enter your email and password, and click Download. On the
resulting page, click the MNE-2.7.0-3106-Linux-x86_64.tar.gz link.
Once the download is finished, place this file in the provision directory