debian/0000755000000000000000000000000012223745362007174 5ustar debian/control0000644000000000000000000000300712223744651010577 0ustar Source: mrtrix Priority: extra Maintainer: NeuroDebian Team Uploaders: Michael Hanke , Yaroslav Halchenko Build-Depends: debhelper (>= 7.0.50~), liboctave-dev, libgsl0-dev, python, pkg-config, libgtkmm-2.4-dev, libgtkglext1-dev, imagemagick, matlab-support-dev Standards-Version: 3.9.4 Section: science Homepage: http://www.brain.org.au/software/mrtrix Vcs-Browser: http://git.debian.org/?p=debian-med/mrtrix.git Vcs-Git: git://git.debian.org/git/debian-med/mrtrix.git Package: mrtrix Section: science Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: mrtrix-doc, octave, matlab-support Description: diffusion-weighted MRI white matter tractography Set of tools to perform diffusion-weighted MRI white matter tractography of the brain in the presence of crossing fibres, using Constrained Spherical Deconvolution, and a probabilisitic streamlines algorithm. Magnetic resonance images in DICOM, ANALYZE, or uncompressed NIfTI format are supported. Package: mrtrix-doc Section: doc Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends} Description: documentation for mrtrix Set of tools to perform diffusion-weighted MRI white matter tractography of the brain in the presence of crossing fibres, using Constrained Spherical Deconvolution, and a probabilisitic streamlines algorithm. Magnetic resonance images in DICOM, ANALYZE, or uncompressed NIfTI format are supported. . This package provides the documentation in HTML format. debian/mrtrix.links.in0000644000000000000000000000015111715144253012162 0ustar usr/lib/mrtrix/bin/mrview usr/bin/mrview /usr/share/man/man1/mrtrix.1.gz /usr/share/man/man1/mrview.1.gz debian/source/0000755000000000000000000000000011365701111010462 5ustar debian/source/format0000644000000000000000000000001411365701111011670 0ustar 3.0 (quilt) debian/mrtrix-doc.install0000644000000000000000000000004411365701111012640 0ustar doc/* usr/share/doc/mrtrix-doc/html debian/mrtrix.menu0000644000000000000000000000036212221332361011375 0ustar ?package(mrtrix): \ needs="X11" \ section="Applications/Science/Medicine" \ title="MRView" \ longtitle="MRI Tractography Viewer" \ icon="/usr/share/pixmaps/mrtrix.xpm" \ command="/usr/bin/mrview" \ hints="MRI,DTI" debian/patches/0000755000000000000000000000000012223744624010623 5ustar debian/patches/series0000644000000000000000000000005311754421726012041 0ustar debian_build_cfg glib-single-include.patch debian/patches/precise-dsc-patch-octave_deps0000777000000000000000000000000012223744624023514 2lucid-dsc-patch-octave_depsustar debian/patches/debian_build_cfg0000644000000000000000000000333112223741227013762 0ustar Description: Change buildsystem setup for Debian We cannot use --march, because we need to support many of them -- not even 'native', as it will over-optimize for the build machine. We set an RPATH to let binaries find the private shared lib. This is safe, because the shared library is built by and shipped in the same package as the binaries. Forwarded: not-needed Author: Michael Hanke --- a/sysconf/linux.py +++ b/sysconf/linux.py @@ -6,7 +6,7 @@ lib_suffix = '.so' cpp = [ 'g++', '-c', '$flags$', '$gtk$', '$path$', '$src$', '-o', '$obj$' ] -cpp_flags = [ '-Wall', '-march=native', '-fPIC', '-fno-strict-aliasing', '-DGL_GLEXT_PROTOTYPES', '-DUSE_TR1' ] +cpp_flags = [ '-Wall', '-fPIC', '-fno-strict-aliasing', '-DGL_GLEXT_PROTOTYPES', '-DUSE_TR1' ] ld = [ 'g++', '$flags$', '$path$', '$obj$', '$mrtrix$', '$gsl$', '$gtk$', '$lz$', '-o', '$bin$' ] ld_flags = [] @@ -16,7 +16,7 @@ ld_lib_flags = [] cpp_flags_debug = cpp_flags + [ '-g' ] -ld_flags_debug = ld_flags + [ '-g' ] +ld_flags_debug = ld_flags + [ '-g', '-Wl,--rpath=/usr/lib/mrtrix/lib' ] ld_lib_flags_debug = ld_lib_flags + [ '-g' ] cpp_flags_profile = [ '-pg' ] + cpp_flags_debug --- a/build +++ b/build @@ -1,4 +1,4 @@ -#!/usr/bin/python2 +#!/usr/bin/python import platform, sys, os, time, threading, subprocess, shutil, stat @@ -177,12 +177,12 @@ if verbose: print svn_revision svn_revision = '#define SVN_REVISION ' + svn_revision + '\n' + if svn_revision != open(svn_revision_file).read(): + with open(svn_revision_file, 'wb') as fd: + fd.write (svn_revision) except: pass -if svn_revision != open(svn_revision_file).read(): - with open(svn_revision_file, 'wb') as fd: - fd.write (svn_revision) debian/patches/glib-single-include.patch0000644000000000000000000000033312221327714015453 0ustar --- a/lib/file/dicom/select_cmdline.cpp +++ b/lib/file/dicom/select_cmdline.cpp @@ -24,6 +24,7 @@ */ +#include #include "file/dicom/image.h" #include "file/dicom/series.h" #include "file/dicom/study.h" debian/patches/lucid-dsc-patch-octave_deps0000644000000000000000000000065012223744564016010 0ustar diff --git a/debian/control b/debian/control index 30536d4..f23e8d1 100644 --- a/debian/control +++ b/debian/control @@ -3,7 +3,7 @@ Priority: extra Maintainer: NeuroDebian Team Uploaders: Michael Hanke , Yaroslav Halchenko Build-Depends: debhelper (>= 7.0.50~), - liboctave-dev, + octave3.2-headers | octave-headers, libgsl0-dev, python, pkg-config, debian/patches/squeeze-dsc-patch-octave_deps0000777000000000000000000000000012223744615023543 2lucid-dsc-patch-octave_depsustar debian/mrtrix.manpages0000644000000000000000000000002011366031725012224 0ustar debian/mrtrix.1 debian/mrtrix.install0000644000000000000000000000022211715143331012076 0ustar bin/* usr/lib/mrtrix/bin lib/*.so usr/lib/mrtrix/lib mrtrix.xpm usr/share/pixmaps debian/*.desktop usr/share/applications matlab usr/share/mrtrix debian/mrtrix.desktop0000644000000000000000000000040212221332343012075 0ustar [Desktop Entry] Encoding=UTF-8 GenericName=MRI Tractography View Name=MRview Exec=mrview %F TryExec=mrview Type=Application Terminal=false Categories=Education;Graphics;Science;DataVisualization;MedicalSoftware;GTK;Viewer; Icon=/usr/share/pixmaps/mrtrix.xpm debian/rules0000755000000000000000000000165611754417735010274 0ustar #!/usr/bin/make -f # -*- makefile -*- # get octave paths (have to build-depend on octave-headers) include /usr/share/octave/debian/defs.make # same for Matlab include /usr/share/matlab/debian/defs.make # one ring to rule them all ... %: dh $@ override_dh_auto_build: ./build -verbose -debug -system=linux # build icon convert icons/mrtrix.xpm -resize 32x32 mrtrix.xpm override_dh_auto_install: dh_auto_install cp debian/mrtrix.links.in debian/mrtrix.links echo "/usr/share/mrtrix/matlab $(MATLAB_MDIR)/mrtrix" >> debian/mrtrix.links echo "/usr/share/mrtrix/matlab $(MDIR)/mrtrix" >> debian/mrtrix.links # we want immediately useable docs and example data, they are in a dedicated # package already override_dh_compress: dh_compress -X.html override_dh_clean: ./build -system=linux clean find . -name '*.pyc' -delete -rm mrtrix.xpm dh_clean @rm -f debian/mrtrix.links override_dh_shlibdeps: dh_shlibdeps -l $(CURDIR)/lib debian/compat0000644000000000000000000000000211365701111010360 0ustar 7 debian/README.Debian0000644000000000000000000000120211366031725011226 0ustar MRtrix for Debian ----------------- All MRtrix programs are installed in /usr/lib/mrtrix/bin (due to too generic names of some of them, e.g. 'average'). You either have to call them with their full path, or extend the search path by this directory. The MRtrix documentation has information on how to do that for a number of popular environments. Please note that it is not necessary to modify LD_LIBRARY_PATH -- despite the advice in the MRtrix manual. For convenience, 'mrview' is directly avialable in /usr/bin and is also listed in Desktop environment menus. -- Michael Hanke Wed, 30 Sep 2009 21:34:23 +0200 debian/mrtrix.10000644000000000000000000000223611366031725010604 0ustar .TH MRTRIX "1" "April 2010" "MRtrix" "User Commands" .SH NAME MRtrix \- diffusion-weighted MRI white matter tractography .SH DESCRIPTION MRtrix is a set of tools to perform diffusion-weighted MRI white matter tractography of the brain in the presence of crossing fibres, using Constrained Spherical Deconvolution, and a probabilisitic streamlines algorithm. Magnetic resonance images in DICOM, ANALYZE, or uncompressed NIfTI format are supported. .SH "DEBIAN" All MRtrix programs are installed in /usr/lib/mrtrix/bin. You either have to call them with their full path, or extend the search path by this directory. The MRtrix documentation has information on how to do that for a number of popular environments. Please note that it is not necessary to modify LD_LIBRARY_PATH -- despite the advice in the MRtrix manual. .SH "AUTHOR" MRtrix has been written by J\-Donald Tournier (d.tournier@brain.org.au) .PP This manual page was written by Michael Hanke , for the Debian project (but may be used by others). .SH "SEE ALSO" The full MRtrix user manual is provided by the mrtrix-doc package. .TP \fBMRtrix Homepage:\fR http://www.brain.org.au/software/mrtrix debian/copyright0000644000000000000000000000200211365701111011107 0ustar Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat Upstream-Name: MRtrix Upstream-Source: http://www.brain.org.au/software/mrtrix Files: * Copyright: Copyright 2008-2010 Brain Research Institute, Melbourne, Australia Written by J-Donald Tournier License: GPL-3 On Debian systems the full text of the GNU General Public License can be found in the `/usr/share/common-licenses/GPL-3' file. Files: lib/file/nifti1.h Copyright: Copyright 1986-1995, Biomedical Imaging Resource, Mayo Foundation License: Public Domain This header files is shipped with the 'nifticlib' source package in Debian. Some fractions have been taken from a former 'dbh.h' header that was copyright of the entity mentioned above, but have been subsequently placed into the public domain. Files: debian/* Copyright: Copyright 2010, Michael Hanke License: GPL-3 On Debian systems the full text of the GNU General Public License can be found in the `/usr/share/common-licenses/GPL-3' file. debian/changelog0000644000000000000000000000405512223745362011052 0ustar mrtrix (0.2.11-1) unstable; urgency=low * New upstream release. * Remove obsolete DM upload flag from debian/control. * Bumped Standards-version to 3.9.4 -- no changes necessary. * Use an absolute patch for the desktop icon. * Patch build script to use /usr/bin/python as interpreter. * Add backport patches for Octave dependencies prior Octave 3.6.1 -- Michael Hanke Fri, 27 Sep 2013 11:34:44 +0200 mrtrix (0.2.10-2) unstable; urgency=low [ Rafael Laboissiere ] * debian/control: + Build-depend on liboctave-dev (Closes: #666732). [ Michael Hanke ] * Bumped Standards-version to 3.9.3 -- no changes necessary. * Add patch for glib 2.32 transition (Closes: #665582) -- Michael Hanke Tue, 15 May 2012 11:39:26 +0200 mrtrix (0.2.10-1) unstable; urgency=low * New upstream release. Among other changes: - new binary for selecting tracks according to inclusion/exclusion ROIs - fix bug in transform re-jigging code to handle 45° oblique orientations * Install Matlab/Octave components. -- Michael Hanke Fri, 10 Feb 2012 08:37:17 +0100 mrtrix (0.2.9-1) unstable; urgency=low * New upstream release. * Updated maintainer email. * Bumped Standards-version to 3.9.2 -- no changes necessary. -- Michael Hanke Sun, 22 May 2011 08:33:48 -0400 mrtrix (0.2.8-3) unstable; urgency=low * Another attempt to close #583206 -- clean target also needs enforces system type (Closes: #583206). -- Michael Hanke Wed, 26 May 2010 20:38:28 -0400 mrtrix (0.2.8-2) unstable; urgency=low * Enforce build system type 'linux' to prevent FTBFS on kfreebsd* (Closes: #583206). * Switch maintainer to NeuroDebian Team. -- Michael Hanke Wed, 26 May 2010 09:44:37 -0400 mrtrix (0.2.8-1) unstable; urgency=low * Initial Debian packaging based on debhelper's "dh" and using the new source package format 3.0 (quilt). Closes: #579470. -- Michael Hanke Sun, 25 Apr 2010 12:47:51 -0400