Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information.


The brainbundler repository contains the sources for two programs, which are both compiled using Qt (see for QT creator, or compile using qmake / make).


Bundler is a mean-shift-bundling command-line tool. It takes a binary 3D graph as the input, and outputs a .fib (binary vtk-file used in fiber tracking software). The input can either be two ascii files (one with coordinates, the other describing connections); or a .fib-file, which only contains straight edges without intermediate points.


bundler (-nodes "nodesfile" -cons "connectionsfile" / -fib ".fib-file") [-c_thr "compatibility threshold"] [-start_i "iterations in 1st cycle"] [-numcycles "number of cycles"]

Input files

Both ascii files and .fib files can be used for loading data into Bundler.

Ascii File-Formats:

The file formats for the ascii files are as follows:

The nodes file contains three coordinates (x,y,z) for each node on each line:

x0 y0 z0
x1 y1 z1
x2 y2 z2
x3 y3 z3

The list of connections contains pairs of indices in the coordinate file. Note that the first line in that file is referred to as node 0:

0 3
2 3
4 1

Converting ascii to .fib

To convert a pair of ascii-files to a single .fib-file, use the following command:

bundler -nodes "nodefile" -cons "connectionsfile" -numcycles 0


-c_thr: The compatibility threshold (default 0.8). This value determines how compatible two edges should be in order to move towards a common center of gravity. c_thr is responsible for how many distinct bundles emerge from the bundling: Too low values make everything bundle together, while too high values leave too many edges unbundled.

-start_i: Number of iterations in the first cycle; every following cycle has one iteration less. This parameter, like numcycles, influences the shape of the bundles.

-numcycles: Number of cycles. This parameter determines the shape of the bundles, as well as the number of subdivision points.

-bell: Width of the Gaussian kernel used to calculate the weights for the mean shift (default 5).

-smooth: Number of additional subdivision steps without shifting after the bundling (default 3). Determines how smooth the final connections appear.

fibviewer a simple viewer for .fib-files. Basic usage is as follows:

fibviewer ".fib-file"

This would also be the place to start if you want to bundle your own data in a different format: Subclassing "Connections" should make it easy to look at data, and then export it to a .fib format file.

For an example, see "artificialconnections". It can be loaded with the following command:

fibviewer artificial

In order to write a .fib-File, which can then be bundled with Bundler:

fibviewer artificial -writefib

The following can be used to export the bundled connections as .obj files, for example to import them in 3D rendering software like Blender:

fibviewer artificial.fib -writeobj