List of MRtrix3 environment variables

MRTRIX_CONFIGFILE

This can be used to set the location of the system-wide configuration file. By default, this is /etc/mrtrix.conf. This can be useful for deployments where access to the system’s /etc folder is problematic, or to allow different versions of the software to have different configurations, etc.

MRTRIX_NOSIGNALS

If this variable is set to any value, disable MRtrix3’s custom signal handlers. This may sometimes be useful when debugging. Note however that this prevents the deletion of temporary files when the command terminates abnormally.

MRTRIX_NTHREADS

set the number of threads that MRtrix3 applications should use. This overrides the automatically determined number, or the NumberOfThreads setting in the configuration file, but will be overridden by the ENVVAR -nthreads command-line option.

MRTRIX_QUIET

Do not display information messages or progress status. This has the same effect as the -quiet command-line option.

MRTRIX_RNG_SEED

Set the seed used for the random number generator. Ordinarily, MRtrix applications will use random seeds to ensure repeat runs of stochastic processes are never the same. However, when experimenting or debugging, it may be useful to explicitly set the RNG seed to ensure reproducible results across runs. To do this, set this variable to a fixed number prior to running the command(s).

Note that to obtain the same results from a multi-threaded command, you should also disable multi-threading (using the option -nthread 0 or by setting the MRTRIX_NTHREADS environment variable to zero). Multi-threading introduces randomness in the order of execution, which will generally also affect the reproducibility of results.

MRTRIX_TMPFILE_DIR

This has the same effect as the TmpFileDir configuration file entry, and can be used to set the location of temporary files (as used in Unix pipes) for a single session, within a single script, or for a single command without modifying the configuration file.

MRTRIX_TMPFILE_PREFIX

This has the same effect as the TmpFilePrefix configuration file entry, and can be used to set the prefix for the name of temporary files (as used in Unix pipes) for a single session, within a single script, or for a single command without modifying the configuration file.