@blezek Thanks, I can’t reproduce the problem though.
Could you check if there are differences between /usr/local/Cellar/mrtrix3/0.3.15-532-gc27886f_3/share/mrtrix3/config and ~/Source/mrtrix3/config?
My config (in /usr/local/Cellar/mrtrix3/0.3.15-532-gc27886f_3/share/mrtrix3) is:
# configure output:
#
# MRtrix build type requested: debug with asserts
#
# Detecting OS: darwin
# OS X deployment target: 10.12
# Checking for C++11 compliant compiler [clang++]: 4.2.1 - 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: 1.2.8
# Checking for Eigen 3 library: 3.3.3
# Checking Eigen 3 memory alignment requirements: OK
# Checking shared library generation: yes
# Checking for Qt moc: moc (version 5.8.0)
# Checking for Qt qmake: qmake (version 5.8.0)
# Checking for Qt rcc: rcc (version 5.8.0)
# Checking for Qt: 5.8.0
PATH = r'/Users/mp/.pyenv/pyenv/bin:/usr/local/Homebrew/Library/Homebrew/shims/super:/usr/local/opt/pkg-config/bin:/usr/local/opt/python/bin:/usr/local/opt/qt/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/opt/qt5/bin'
obj_suffix = '.o'
exe_suffix = ''
lib_prefix = 'lib'
lib_suffix = '.dylib'
cpp = [ 'clang++', '-c', 'CFLAGS', 'SRC', '-o', 'OBJECT' ]
cpp_flags = [ '-std=c++11', '-mno-avx', '-DMRTRIX_MACOSX', '-fPIC', '-mmacosx-version-min=10.12', '-DMRTRIX_WORD64', '-isystem', '/usr/local/Cellar/eigen/3.3.3/include/eigen3', '-Wall', '-O0', '-g', '-D_GLIBCXX_DEBUG=1', '-D_GLIBCXX_DEBUG_PEDANTIC=1' ]
ld = [ 'clang++', 'OBJECTS', 'LDFLAGS', '-o', 'EXECUTABLE' ]
ld_flags = [ '-mmacosx-version-min=10.12', '-lz', '-g' ]
runpath = '-Wl,-rpath,@loader_path/'
ld_enabled = True
ld_lib = [ 'clang++', 'OBJECTS', 'LDLIB_FLAGS', '-o', 'LIB' ]
ld_lib_flags = [ '-dynamiclib', '-install_name', '@rpath/LIBNAME', '-mmacosx-version-min=10.12', '-mmacosx-version-min=10.12', '-lz', '-g' ]
eigen_cflags = [ '-isystem', '/usr/local/Cellar/eigen/3.3.3/include/eigen3' ]
moc = 'moc'
rcc = 'rcc'
qt_cflags = [ '-pipe', '-stdlib=libc++', '-isysroot', '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk', '-mmacosx-version-min=10.9', '-g', '-std=gnu++11', '-fPIC', '-DQT_OPENGL_LIB', '-DQT_SVG_LIB', '-DQT_WIDGETS_LIB', '-DQT_GUI_LIB', '-DQT_CORE_LIB', '-isystem', '/usr/local/Cellar/qt/5.8.0_2/lib/QtOpenGL.framework/Headers', '-isystem', '/usr/local/Cellar/qt/5.8.0_2/lib/QtSvg.framework/Headers', '-isystem', '/usr/local/Cellar/qt/5.8.0_2/lib/QtWidgets.framework/Headers', '-isystem', '/usr/local/Cellar/qt/5.8.0_2/lib/QtGui.framework/Headers', '-isystem', '/usr/local/Cellar/qt/5.8.0_2/lib/QtCore.framework/Headers', '-isystem', '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/System/Library/Frameworks/OpenGL.framework/Headers', '-isystem', '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/System/Library/Frameworks/AGL.framework/Headers', '-isystem', '/usr/local/Cellar/qt/5.8.0_2/mkspecs/macx-clang', '-F/usr/local/Cellar/qt/5.8.0_2/lib' ]
qt_ldflags = [ '-headerpad_max_install_names', '-stdlib=libc++', '-Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk', '-mmacosx-version-min=10.9', '-F/usr/local/Cellar/qt/5.8.0_2/lib', '-framework', 'QtOpenGL', '-framework', 'QtWidgets', '-framework', 'QtGui', '-framework', 'QtCore', '-framework', 'DiskArbitration', '-framework', 'IOKit', '-framework', 'QtSvg', '-framework', 'OpenGL', '-framework', 'AGL' ]
nogui = False
). I’m trying to use Freesurfer 6 