MI-Brain is now AVAILABLE!

MI-Brain is the next generation diffusion MRI visualisation tool.
It comes packed with state‑of‑the‑art features.

MI-Brain is freely available for academic, research and non-commercial use.

If you want to use it for other purposes,
please get in touch with our team for a quote.

Features

• Streamline visualization
• Virtual streamlines dissection
• ROI tools
• Streamline cutting
• High resolution screenshots
• VTK-based
• Handles .trk and .tck
• World coords
• Peaks visualization
• RGB visualization
• Surface coloring
• Local, endpoints, shuffle, single and from
anatomy streamline coloring
• Create surface from ROI
• Bounding object, mask and surface streamline
filtering
• Segmentation tool​
• And more…

FAQ

How to install?

  • Linux: In a terminal, extract the .tar.gz release archive and execute installer.sh. Wait for the installer to finish and then launch MI-Brain using MI-Brain.sh
  • Windows: Download vcredist_x64.exe (also available from the MI-Brain download section) and MI-Brain-*.exe. Double-click on the vcredist_x64.exe to install the Microsoft Visual C++ 2015 Redistributable and then double-click on MI-Brain-*.exe and follow the instructions
  • macOS: Open the .dmg file and drag the MI-Brain icon in the Application folder

I downloaded a new version, installed it but the software won’t start. What can I do?

  • Linux: Delete ~/.local/share/Imeka and/or start the application with --BlueBerry.clean
  • Windows: Delete C:\Users\USER\AppData\Local\Imeka and/or start the application with /BlueBerry.clean
  • macOS: Delete ~/Library/Application Support/Imeka and/or start the application with MI-Brain.app/Contents/MacOS/MI-Brain --BlueBerry.clean

How to uninstall?

  • Linux: Delete the folder containing the application
  • macOS: Drag the application into the trash bin
  • Windows: Uninstall the application like any other Windows application using (Start - Settings - Apps & Features - ...)

Do I need to be connected to Internet to install/use MI-Brain?

You need to be connected to the Internet only during the MI-Brain installation and if you want to get software update notices. Otherwise, it's perfectly fine to use MI-Brain offline.

My tractograms/anatomies are not aligned. Why?

The MI-Brain software works in LPS world coordinate as opposed to voxel mm coordinates (TrackVis, Fibernavigator). RAS data will be transformed to LPS internally. Make sure your data is aligned in world coordinates.

What’s the peak image format that’s needed to perform RTT?

Peaks images are conceptually vector images in 3D. However, in practice, they are represented as 4D float images. MI-Brain would present them (Right-click on a node - Details...) as such:

Image

 

Dimension: 4

 

Dimensions: width height depth (3 | 6 | 9 | 12 | 15)

 

ComponentType: float

The 4th dimension is used to store the vectors. Each voxel contains from 0 to 5 3D-vectors (hence the multiple of 3). The data for a voxel is always packed in the form XYZXYZXYZXYZXYZ. The absence of information is declared with NANs or a zero-vector.

I have some raw diffusion MRI data. Can I process them with MI-Brain?

No. MI-Brain is a visualization/exploration software only. Imeka offers diffusion MRI processing services at https://www.imeka.ca/services. Contact us via info@imeka.ca for more details

Is MI-Brain robust to compressed streamlines?

Most of the algorithms in MI-Brain, such as streamline filtering and streamline cutting, are robust to compressed streamlines

Can I use the software commercially?

Only if you bought a license from Imeka. To do so, please contact info@imeka.ca

I think I found a bug! How can I report it to you?

Please send a complete bug report at mibrain@imeka.ca

I have a feature request! How can I contact you?

Please send an email to mibrain@imeka.ca

Will the software work on [hardware XYZ]?

Maybe. We have limited hardware resources and most of our users use Intel processors and NVIDIA graphic cards. Make sure to update your graphic card drivers to the latest version. Additionally, on Linux systems, we recommend using the closed source drivers instead of the Nouveau family of drivers.

Do you support 32bits OSes/hardware?

No

What macOS versions are supported?

We tested the software only on OS X 10.11 El Capitan and OS X 10.12 Sierra. It probably works on OS X 10.10 Yosemite too.

On macOS, MI-Brain can't be opened because it's from an unidentified developer. Why?

macOS tries to protect you from “unsafe” applications. To open the application, Cmd+Right-Click on MI-Brain icon - Open - Open

What Linux versions are supported?

We mostly tested the software on Ubuntu 14.04 and Ubuntu 16.04 but it’s also known to work on Debian 8, Mint 17 and Mint 18.

What Windows versions are supported?

MI-Brain is known to work on Windows 7, 8 and 10

Can I use the software in a virtual machine (VM)?

This is not recommended and we don’t support it. MI-Brain relies heavily on the 3D capabilities of the graphic card and needs bare metal access

Cheat sheet

Common
Open file: Ctrl/Cmd-o

Exit application: Ctrl/Cmd-q

Save selection: Ctrl/Cmd-s

2D/3D Navigation
Zoom: Hold right mouse button

Move crosshair: Left mouse button

Translate: Middle mouse button

Selection object
Move: Hold Ctrl/Cmd + Left mouse button

Resize: Hold Ctrl/Cmd + Right mouse button

Rotate: Hold Ctrl/Cmd + Middle mouse button

3D view

Anterior: a

Posterior: p

Left: l

Right: r

Superior: s

Interior: i

Primer

An illustrated guide to MI-Brains main functions

Tutorial Videos

A series of videos to help you get acquainted with MI-Brain

Fiber Web

Fiber-Web is the next generation diffusion MRI visualisation tool, directly in your browser. It comes packed with state-of-the-art features.