Features
General
⊷ Plot more than one modality in the same time: fMRI/MEG/EEG source activity with electrodes and connectivity.
⊶ Filter the selected sources (EEG/MEG evoked response for cortical labels, electrodes, etc) according to selected function (e.g. RMS between two conditions).
⊷ Play activity over time interactively. The activity is being plotted on the brain and shown as time-series graphs.
⊶ Report generator dynamically modified from HTML template with figures created on MMVT.
⊷ Create a 3D brain, including the cortex and the subcortical structures, from FreeSurfers MRI scan reconstruction.
⊶ Interactive 3D view of the brain, including rotation, zooming and shifting. The user can also hide each hemisphere and subcortical region.
⊷ Parcellae the cortex into cortical labels.
◦ Homogeneously color all labels or each label separately.
◦ Color the contours of all labels or each label separately.
⊶ Interactive slice viewer that is synched with the 3D brain model, supports MRI and CT.
⊷ Import the pial surface on the slice viewer which is reconstructed from the MRI scan.
⊶ 3D slicer divides the 3D brain model in 3 different axis viewpoints.
⊷ Morph between the pial surface, the inflated surface and the flat surface.
⊶ Calculate the skull thickness in an interactive panel for surgery planning.
⊷ Manually color different parts of the cortex and subcortical structures.
⊶ Customize the color bar appearance and color palette.
Anatomy
fMRI & PET
⊷ Load a 2D niftii file, and plot it on the brain.
⊶ Project a 3D niftii file on the cortex and subcortical regions and plot it.
⊷ Run FsFast on raw data and plot the resulting contrast map.
⊶ Cluster a contrast map and visualize interactively the different clusters while showing the information about each cluster (size, max value, intersected cortical labels, etc.).
⊷ Clean and analyze resting state data.
◦ Calculate the time-series for the cortical labels and subcortical regions.
◦ Calculate the time-series for the cortical and subcortical vertices.
⊷ Clean and filter raw data.
⊶ Calculate the evoked responses (both on task and rest data):
◦ On sensors level and interactively visualize them.
◦ On source space (using MNE, dSPM, sLORETA and more) per cortical label or vertice and interactively visualize.
⊷ Cluster source space activity into cortical ROIs and interactively visualize them.
⊶ Load an existing stc file and plot it on the cortex.
⊷ Visualize EEG 3D topoplot.
EEG & MEG
Depth
Electrodes
⊷ Visualize the electrodes in the subject’s MRI space and color them according to their activity.
⊶ Analyze each electrode source according to the subject’s anatomy and visualize the probabilistic model on the cortex and subcortical regions.
⊷ Snap grids (ECoG) electrodes on the cortical surface.
⊶ Import and analyze edf files.
⊷ Automatic method for detecting depth electrodes from a CT scan, and group them together into different leads (~95% accuracy).
⊶ Visualize live stream data from a remote server or device.
⊷ Calculate connectivity between fMRI/MEG cortical labels and interactively visualize it on the 3D brain.
⊶ Calculate connectivity between invasive electrodes and interactively visualize it on the 3D brain.
⊷ Calculate degree of connectivity fMRI/MEG cortical labels and interactively visualize it.
Connectivity
Render
⊷ Render the 3D brain using the Blender “cycles” engine, including transparency, lighting, material types and more.
⊶ Render videos including the time series graph.
⊷ Create high resolution figures one at a time or from all perspectives at once.
⊶ Create high resolution videos including an option to preset automated rotation angle.
⊷ Import the outer skin, which is reconstructed from the MRI scan.
⊷ Run scripts in the background without using the GUI (e.g. save activity in different perspectives, render movies, and more).
⊶ Call MMVT object from a script, while Blender is running in the background on a remote server (can be run in Jupyter notebooks).
Scripts
File Types Supported as Input
⊷ Anatomy (MRI/CT): dicoms and nii/mgz files.
⊶ fMRI / PET: nii/mgz files.
⊷ EEG / MEG: fif, stc.
⊶ Electrodes: edf, or mat/npz files with the relevant fields
⊷ Connectivity: mat/npz with the relevant fields.
⊶ Visualize live stream data from a remote server or device.
⊷ mne-python
⊶ FreeSurfer, Freeview and fsFast
⊷ SPM