MMVT features

General MMVT features

• 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.

Anatomy

• 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.

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.

EEG & MEG

• 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.

Invasive 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.

Connectivity

• 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.

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.

Scripts

• 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).

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.

Compatibility With Other Softwares

• mne-python
• FreeSurfer, Freeview and fsFast
• SPM