An illustrated guide to MI-Brains main functions
• Streamline visualization
• Virtual streamlines dissection
• ROI tools
• Streamline cutting
• High resolution screenshots
• 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
• Segmentation tool
• And more…
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:
Dimensions: width height depth (3 | 6 | 9 | 12 | 15)
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?
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 email@example.com
I think I found a bug! How can I report it to you?
Please send a complete bug report at firstname.lastname@example.org
I have a feature request! How can I contact you?
Please send an email to email@example.com
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?
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.
libpng12 is not pre-installed on Ubuntu 18.04, you need to do it yourself. You can download the .deb from this link: security.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1.1_amd64.deb
and install it with the command: sudo dpkg -i libpng12-*.deb
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
Open file: Ctrl/Cmd-o
Exit application: Ctrl/Cmd-q
Save selection: Ctrl/Cmd-s
Zoom: Hold right mouse button
Move crosshair: Left mouse button
Translate: Middle mouse button
Move: Hold Ctrl/Cmd + Left mouse button
Resize: Hold Ctrl/Cmd + Right mouse button
Rotate: Hold Ctrl/Cmd + Middle mouse button