Linux & Mac OS Installation
Create a folder named “mmvt_root”.
In case you want to reconstruct your own subjects or view your data also in slices mode, you should install the dev version of Freesurfer (look for Development Version). After that, source Freesurfer (if you have access to the Martinos center cluster, you should just source the dev version: source /usr/local/freesurfer/nmr-dev-env).
Before running the mmvt setup, be sure that by typing ‘python’ in the terminal you are running python 3.4 and above. You can also create an alias to python 3.
Run the mmvt setup from the project’s code folder:
python -m src.setup
Setup Script Steps
Installation of all the necessary python libraries.
If the script won’t find the Blender installation, it’ll ask you to locate it.
In default, the script will create all its folders under the mmvt_root folder, unless you set the -d flag to 0. If so, it will ask you where to create the following folders (in brackets the folder’s default name):
subjects: A folder with several files from the FreeSurfer recon-all files. The preprocessing steps write to this folder, so it’s recommended not to use your recon-all folder, rather than creating another subjects folder, and set the
flag to your original recon-all folder. The necessary files will be copied automatically.
mmvt (“mmvt_blend”): The folder where you all the MMVT files are going to be stored. The blender files (*.blend) will be placed in this folder. For each subject, a folder will be created and the output of the preprocessing scripts will be stored in that folder.
meg (“meg”) / eeg (“eeg”) / fMRI (“fMRI”) / electrodes (“electrodes”): Where you are going to store the different data files. For the modalities you aren’t going to use, just press cancel.
After Running the Setup Script
Create a script for running Blender from the terminal (and also source Freesurfer if you’ve installed it). You can find examples in misc/launch_mmvt for Linux and Mac. You can find more information about how to run Blender from the terminal here.
How to Create the Links Manually
In case you don’t want to use the gui for selecting your folders, before running the setup, run this command:
python -m src.setup -f create_links_csv
That will create the skeleton for the links.csv file in the links folder. Edit it manually, and run the setup.