Configuration file

The behaviour of a number of aspects of MRtrix3 can be controlled by the user via the MRtrix3 configuration file. Note, that this file is distinct from the build configuration file that is generated as part of the MRtrix3 installation, but rather is used to specify default settings for a number of parameters, many of which relate to data visualisation when using mrview.

For all available configurable options, please refer to the configuration file options page.


MRtrix3 applications will attempt to read configuration information from a two locations. The system-wide configuration file /etc/mrtrix.conf is read first if present, followed by the user-specific configuration ~/.mrtrix.conf. If both system and user-specific configuration files exist, the parameters specified in the two configuration files will be aggregated, with user-specified configuration options taking precedence in the case of a conflict. In the case that a particular configuration parameter is not defined, MRtrix3 will resort to hard-coded defaults.


The configuration files are text files, with each line containing a key: value pair. For example

AnalyseLeftToRight: false
NumberOfThreads: 2


Key names are case-sensitive.

The value entry may be interpreted by MRtrix3 applications as either:

  • Boolean: allowed values here are true or false

  • Integer: any integer value

  • Floating-point: any floating-point value

  • Text: any text string, without any further interpretation

The list of all configuration file options can be found here.