1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
|
.. _environment_variables:
##########################################
List of MRtrix3 environment variables
##########################################
.. envvar:: DICOM_ID
when reading DICOM data, match the PatientID entry against
the string provided
.. envvar:: DICOM_PATIENT
when reading DICOM data, match the PatientName entry against
the string provided
.. envvar:: DICOM_SERIES
when reading DICOM data, match the SeriesName entry against
the string provided
.. envvar:: DICOM_STUDY
when reading DICOM data, match the StudyName entry against
the string provided
.. envvar:: 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.
.. envvar:: 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.
.. envvar:: 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.
.. envvar:: MRTRIX_NTHREADS
set the number of threads that MRtrix3 applications should use.
This overrides the automatically determined number, or the
:option:`NumberOfThreads` setting in the configuration file, but
will be overridden by the ENVVAR ``-nthreads`` command-line option.
.. envvar:: 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.
.. envvar:: 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.
.. envvar:: 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 :envvar:`MRTRIX_NTHREADS` environment variable to zero).
Multi-threading introduces randomness in the order of execution, which
will generally also affect the reproducibility of results.
.. envvar:: MRTRIX_TMPFILE_DIR
This has the same effect as the :option:`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.
.. envvar:: MRTRIX_TMPFILE_PREFIX
This has the same effect as the :option:`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.
|
