List of MRtrix3 environment variables¶
when reading DICOM data, match the PatientID entry against the string provided
when reading DICOM data, match the PatientName entry against the string provided
when reading DICOM data, match the SeriesName entry against the string provided
when reading DICOM data, match the StudyName entry against the string provided
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
/etcfolder is problematic, or to allow different versions of the software to have different configurations, etc.
Set the default terminal verbosity. Default terminal verbosity is 1. This has the same effect as the
-debug(3) comand-line options.
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.
set the number of threads that MRtrix3 applications should use. This overrides the automatically determined number, or the
NumberOfThreadssetting in the configuration file, but will be overridden by the ENVVAR
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.
Do not display information messages or progress status. This has the same effect as the
-quietcommand-line option. If set, supersedes the MRTRIX_LOGLEVEL environment variable.
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 0or by setting the
MRTRIX_NTHREADSenvironment variable to zero). Multi-threading introduces randomness in the order of execution, which will generally also affect the reproducibility of results.
This has the same effect as the
TmpFileDirconfiguration 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.
This has the same effect as the
TmpFilePrefixconfiguration 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.