Thank you helping me on what information to provide:
Here are the contents of the release/config file
!/usr/bin/python
autogenerated by MRtrix configure script
configure output:
MRtrix build type requested: release
Detecting OS: windows
Checking for C++11 compliant compiler [g++]: 6.3.0 - tested ok
Detecting pointer size: 64 bit
Detecting byte order: little-endian
Checking for variable-length array support: yes
Checking for non-POD variable-length array support: yes
Checking for zlib compression library: 1.2.11
Checking for Eigen 3 library: 3.3.0
Checking Eigen 3 memory alignment requirements: OK
Checking shared library generation: yes
Checking for Qt moc: moc (version 5.6.2)
Checking for Qt qmake: qmake (version 5.6.2)
Checking for Qt rcc: rcc (version 5.6.2)
Checking for Qt: 5.6.2
PATH = r’C:\msys64\mingw64\bin;C:\msys64\home\Orjan\mrtrix3\release\bin;C:\msys64\home\Orjan\mrtrix3\release\lib;C:\msys64\home\Orjan\mrtrix3\scripts;C:\msys64\mingw64\bin;C:\msys64\usr\local\bin;C:\msys64\usr\bin;C:\msys64\usr\bin;C:\Windows\System32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0;C:\msys64\usr\bin\site_perl;C:\msys64\usr\bin\vendor_perl;C:\msys64\usr\bin\core_perl’
obj_suffix = '.o’
exe_suffix = '.exe’
lib_prefix = ''
lib_suffix = '.dll’
cpp = [ ‘g++’, ‘-c’, ‘CFLAGS’, ‘SRC’, ‘-o’, ‘OBJECT’ ]
cpp_flags = [ ‘-std=c++11’, ‘-mno-avx’, ‘-pthread’, ‘-DMRTRIX_WINDOWS’, ‘-mms-bitfields’, ‘-Wa,-mbig-obj’, ‘-march=native’, ‘-DMRTRIX_WORD64’, ‘-isystem’, ‘C:/msys64/mingw64/include/eigen3’, ‘-Wall’, ‘-O2’, ‘-DNDEBUG’ ]
ld = [ ‘g++’, ‘OBJECTS’, ‘LDFLAGS’, ‘-o’, ‘EXECUTABLE’ ]
ld_flags = [ ‘-pthread’, ‘-Wl,–allow-multiple-definition’, ‘-lz’ ]
runpath = ''
ld_enabled = True
ld_lib = [ ‘g++’, ‘OBJECTS’, ‘LDLIB_FLAGS’, ‘-o’, ‘LIB’ ]
ld_lib_flags = [ ‘-pthread’, ‘-shared’, ‘-pthread’, ‘-Wl,–allow-multiple-definition’, ‘-lz’ ]
eigen_cflags = [ ‘-isystem’, ‘C:/msys64/mingw64/include/eigen3’ ]
moc = 'moc’
rcc = 'rcc’
qt_cflags = [ ‘-pipe’, ‘-fno-keep-inline-dllexport’, ‘-march=nocona’, ‘-mtune=core2’, ‘-Wa,-mbig-obj’, ‘-O2’, ‘-std=gnu++0x’, ‘-frtti’, ‘-Wall’, ‘-Wextra’, ‘-fexceptions’, ‘-mthreads’, ‘-DUNICODE’, ‘-DQT_NO_DEBUG’, ‘-DQT_OPENGL_LIB’, ‘-DQT_SVG_LIB’, ‘-DQT_WIDGETS_LIB’, ‘-DQT_GUI_LIB’, ‘-DQT_CORE_LIB’, ‘-DQT_NEEDS_QMAIN’, ‘-isystem’, ‘C:/msys64/mingw64/include/QtOpenGL’, ‘-isystem’, ‘C:/msys64/mingw64/include/QtSvg’, ‘-isystem’, ‘C:/msys64/mingw64/include/QtWidgets’, ‘-isystem’, ‘C:/msys64/mingw64/include/QtGui’, ‘-isystem’, ‘C:/msys64/mingw64/include/QtCore’, ‘-isystem’, ‘release’, ‘-isystem’, ‘C:/msys64/mingw64/share/qt5/mkspecs/win32-g++’ ]
qt_ldflags = [ ‘-Wl,-s’, ‘-Wl,-subsystem,windows’, ‘-mthreads’, ‘-lglu32’, ‘-lopengl32’, ‘-lgdi32’, ‘-luser32’, ‘-lmingw32’, ‘-lqtmain’, ‘-lQt5OpenGL’, ‘-lQt5Svg’, ‘-lQt5Widgets’, ‘-lQt5Gui’, ‘-lQt5Core’ ]
nogui = False
Since I tried reinstalling everything again yesterday just in case (before posting) the version should be the most recent one:
dwi2tensor.exe -version
== dwi2tensor 0.3.15-388-g261e44f8 ==
64 bit release version, built Jan 30 2017, using Eigen 3.3.0
The call is simply:
dwi2tensor -force -mask brainmask.mif -fslgrad bvect bvalt dwi.mif dti.mif
The computer actually shuts down and restarts. It runs around 30% and then smack. This does indeed suggest that there is something not working right on the computer, but it only happens in interaction with the multithreading option in MRtrix3. However, I haven’t tested it thoroughly using other software. ANTs registrations e.g. seem to be running fine. The data is on an internal hard drive. I will try putting the data on an SSD later today. I will also try this Microsoft hotfix.