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_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 theMRTRIX_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.