List of MRtrix3 environment variables

DICOM_ID

when reading DICOM data, match the PatientID entry against the string provided

DICOM_PATIENT

when reading DICOM data, match the PatientName entry against the string provided

DICOM_SERIES

when reading DICOM data, match the SeriesName entry against the string provided

DICOM_STUDY

when reading DICOM data, match the StudyName entry against the string provided

MRTRIX_CLI_PARSE_ONLY

Set the command to parse the provided inputs and then quit if it is set. This can be used in the CI of wrapping code, such as the automatically generated Pydra interfaces. Note that it will have no effect for R interfaces

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_LOGLEVEL

Set the default terminal verbosity. Default terminal verbosity is 1. This has the same effect as the -quiet (0), -info (2) or -debug (3) comand-line options.

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_PRESERVE_PHILIPS_ISO

Do not remove the synthetic isotropically-weighted diffusion image often added at the end of the series on Philips scanners. By default, these images are removed from the series to prevent errors in downstream processing. If this environment variable is set, these images will be preserved in the output.

Note that it can be difficult to ascertain which volume is the synthetic isotropically-weighed image, since its DW encoding will normally have been modified from its initial value (e.g. [ 0 0 0 1000 ] for a b=1000 acquisition) to b=0 due to b-value scaling.

MRTRIX_PRESERVE_TMPFILE

This variable decides whether the temporary piped image should be preserved rather than the usual behaviour of deletion at command completion. For example, in case of piped commands from Python API, it is necessary to retain the temp files until all the piped commands are executed.

MRTRIX_QUIET

Do not display information messages or progress status. This has the same effect as the -quiet command-line option. If set, supersedes the MRTRIX_LOGLEVEL environment variable.

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.