The visualization and exploration of neuroimaging data is important for the analysis of anatomical and functional images and statistical parametric maps. While two-dimensional orthogonal views of neuroimaging data are used to display activity and statistical analysis, real three-dimensional (3d) depictions are helpful for showing the spatial distribution of a functional network, as well as its temporal evolution. For our best knowledge, currently there is no neuroimaging 3d tool which can visualize both MEG, fMRI and invasive electrodes (ECOG, depth electrodes, DBS, etc.). Here we present the multi-modality visualization tool (MMVT). The tool was built for researchers who wish to have a better understanding of their neuroimaging anatomical and functional data. The true power of the tool is by visualizing and analyzing data from multi-modalities. MMVT is built as two separated modules: The first is implemented as an add-on in 'Blender”, an open-source 3d visualization software. The add-on is an interactive graphic interface which enable to visualize functional and statistical data (MEG and/or fMRI) on the cortex and subcortical surfaces, invasive electrodes activity and so on. The tool can also be used for a better 3d visualization of the anatomical data and the invasive electrodes locations. The other module is a standalone software, for importing and preprocessing. The users can select the data they want to import to Blender and how they want to process it. The module support many types of analyzed data, like FsFast (FreeSurfer Functional Analysis Stream) and SPM (Statistical Parametric Mapping) for fMRI, MNE (a software package for processing MEG and EEG) raw data for MEG and FieldTrip (MATLAB software toolbox for neuroimaging analysis) data structures for the invasive electrodes. The users can also reprocess raw data using a wrappers for FaFast and mne-python (a python package for sensor and source-space analysis of MEG and EEG data).
- Resting State fMRI & Cortical labels correlation
- MEG & Electrodes & Coherence
Please go through the installation in this wiki page.
After the installation, you'll enter the yet-not-documented territory. please contact us: npeled@mgh.harvard.edu or ohad.felsenstein@biu.ac.il
The tool itself can run on windows, mac and linux. If you want to connect it to freeview, you'll need to run it only on freesurfer compatible os, meaning linux and mac. Also in the preprocessing tool there are few call to freesurfer, so mainly to create the anatomy files you'll need an os that supports freesurfer. Beside of that, you can use the tool also on windows.
To get started, download and extract colin27 (SPM template brain) into your MMVT folder. Then, run Blender with the script you've created and open colin27.blend file. After that, hover with the mouse on the 3D brain panel, press "space", write "run MMVT addon" and press enter.
The preprocessing tutorial can be found in the wiki.
- Ohad Felsenstein (ohad.felsenstein@biu.ac.il)
- Noam Peled (npeled@mgh.harvard.edu)
This tool is being developed as part of the Transform DBS project. It's sponsored by:
- The U.S. Army Research Office and Defense Advanced Research Projects Agency under Cooperative Agreement Number W911NF-14-2-0045.
- The NCRR (S10RR014978) and NIH (S10RR031599,R01-NS069696, 5R01-NS060918, U01MH093765)
O.Felsenstein and N. Peled et al. (2017). MMVT - Multi-Modality Visualization Tool. GitHub Repository. https://github.com/pelednoam/mmvt DOI:10.5281/zenodo.438343
MMVT is BSD-licenced (3 clause):
This software is OSI Certified Open Source Software.
OSI Certified is a certification mark of the Open Source Initiative.
Copyright (c) 2016, authors of MMVT
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the names of MMVT authors nor the names of any
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
**This software is provided by the copyright holders and contributors
"as is" and any express or implied warranties, including, but not
limited to, the implied warranties of merchantability and fitness for
a particular purpose are disclaimed. In no event shall the copyright
owner or contributors be liable for any direct, indirect, incidental,
special, exemplary, or consequential damages (including, but not
limited to, procurement of substitute goods or services; loss of use,
data, or profits; or business interruption) however caused and on any
theory of liability, whether in contract, strict liability, or tort
(including negligence or otherwise) arising in any way out of the use
of this software, even if advised of the possibility of such
damage.**