debian/0000755000000000000000000000000011736115514007172 5ustar debian/source/0000755000000000000000000000000011421411373010463 5ustar debian/source/format0000644000000000000000000000001411421411373011671 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000000420011622176226011122 0ustar This package was debianized by Michael Hanke on Wed, 16 Aug 2006 02:11:44 +0200. It was downloaded from https://cbi.nyu.edu/public/software/dinifti/ Upstream Author: Valerio Luccio (valerio.luccio@nyu.edu) Copyright: 2005-2011 Valerio Luccio (valerio.luccio@nyu.edu) 2007 New York University License: All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above * copyright notice, this list of conditions and the following * disclaimer in the documentation and/or other materials provided * with the distribution. * Neither the name of New York University nor the names of its * contributors may be used to endorse or promote products derived * from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. The Debian packaging is (C) 2006-2011, Michael Hanke and is licensed under the GPL, see above. On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL'. debian/source.lintian-overrides0000644000000000000000000000020011515411065014035 0ustar # the autotools system is not used to build the package dicomnifti source: outdated-autotools-helper-file config.sub 2005-02-10 debian/gbp.conf0000644000000000000000000000022211651225262010603 0ustar [DEFAULT] # the default branch for upstream sources: upstream-branch = upstream # the default branch for the debian patch: debian-branch = master debian/dirs0000644000000000000000000000001010746156114010046 0ustar usr/bin debian/control0000644000000000000000000000213611622176162010577 0ustar Source: dicomnifti Section: science Priority: optional Maintainer: NeuroDebian Team Uploaders: Michael Hanke , Yaroslav Halchenko Build-Depends: debhelper (>= 7.0.50~), ctn-dev (>> 3.0.6-9), libnifti-dev, cmake, zlib1g-dev Standards-Version: 3.9.2 Homepage: http://cbi.nyu.edu/software/dinifti.php Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/dicomnifti.git Vcs-Git: git://git.debian.org/git/pkg-exppsy/dicomnifti.git XS-DM-Upload-Allowed: yes Package: dicomnifti Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: converts DICOM files into the NIfTI format The dinifti program converts MRI images stored in DICOM format to NIfTI format. The NIfTI format is thought to be the new standard image format for medical imaging and can be used with for example with FSL, AFNI, SPM, Caret or Freesurfer. . dinifti converts single files, but also supports fully automatic batch conversions of complete dicomdirs. Additionally, converted NIfTI files can be properly named, using image series information from the DICOM files. debian/changelog0000644000000000000000000002124711736115514011052 0ustar dicomnifti (2.30.0-1) unstable; urgency=low * New upstream release. Output NIfTI images now have slope and intercept set accordingly in their headers. -- Michael Hanke Sun, 01 Apr 2012 20:14:52 +0200 dicomnifti (2.29.1-1) unstable; urgency=low * New upstream release. -- Michael Hanke Mon, 24 Oct 2011 11:08:54 +0200 dicomnifti (2.28.16-1) unstable; urgency=low * New upstream release. * Bumped Standards-version to 3.9.2, no changes necessary. * Updated debian/copyright. -- Michael Hanke Mon, 15 Aug 2011 13:01:47 +0200 dicomnifti (2.28.15-1) unstable; urgency=low * New upstream release. * Updated maintainer email address. * Bumped Standards-version to 3.9.1, no changes necessary. * Add lintian override regarding outdated autotools files. The package only uses cmake to build the binaries. -- Michael Hanke Tue, 18 Jan 2011 17:21:08 -0500 dicomnifti (2.28.14-2) unstable; urgency=low * Changed maintainer to NeuroDebian Team. * Switch from plain debhelper to 'dh'. * Convert source package format to 3.0 (quilt). * Bumped Standards-version to 3.9.0, no changes necessary. * Add patch to prevent unnecessary package dependency in zlib. -- Michael Hanke Tue, 20 Jul 2010 17:12:46 -0400 dicomnifti (2.28.14-1) unstable; urgency=low * New upstream version. * Updated Debian Standards-version to 3.8.1 (no changes necessary). * Added 'XS-DM-Upload-Allowed: yes' to debian/control. -- Michael Hanke Wed, 08 Apr 2009 12:12:07 +0200 dicomnifti (2.28.11-1) unstable; urgency=low * New upstream version. Fix for GCC 4.3 compatibility (Closes: #462074). -- Michael Hanke Thu, 24 Jan 2008 19:43:26 +0100 dicomnifti (2.28.10-2) unstable; urgency=low * Modified build-deps for libnifti transition. * Bumped Standards-version to 3.7.3, no changes necessary. -- Michael Hanke Thu, 03 Jan 2008 12:09:30 +0100 dicomnifti (2.28.10-1) unstable; urgency=low * New Upstream Version. * Remove patch to prevent fixed sizes for 'int' and 'long' as upstream switched to determine this with CMake dynamically (although it is still not necessary for Debian's CTN library). -- Michael Hanke Fri, 30 Nov 2007 10:59:00 +0100 dicomnifti (2.28.8-1) unstable; urgency=low * New Upstream Version. Fixes a bug where dinifti did not respect the users choice of number of slices (option -s). -- Michael Hanke Sun, 11 Nov 2007 11:20:07 +0100 dicomnifti (2.28.7-1) unstable; urgency=low * New Upstream Version. Changed license to a 3-clause BSD license. -- Michael Hanke Wed, 07 Nov 2007 09:38:35 +0100 dicomnifti (2.28.5-2) unstable; urgency=low * Updated Homepage info in debian/control using the new 'Homepage' field. * Added VCS info to debian/control. -- Michael Hanke Thu, 18 Oct 2007 20:22:40 +0200 dicomnifti (2.28.5-1) unstable; urgency=low * New Upstream Version. Allows for custom naming schemes of image series. (Closes: #446260) -- Michael Hanke Tue, 16 Oct 2007 00:46:55 +0200 dicomnifti (2.28.4-1) unstable; urgency=low * New Upstream bugfix release. * Siemens Vision: fails to read the number of slices, now defaults 1 and user can override this with the '-s' option (Closes: #442013). * GE Elscint: fails to read series' description, only needed with '-d' flag. Now defaults to "" * Build-depend on libniftiio1-dev by default. -- Michael Hanke Mon, 17 Sep 2007 10:38:18 +0200 dicomnifti (2.28.2-1) unstable; urgency=low * New upstream release. NIfTI header value 'nu' is now always set to one instead of the number of channels reported in the DICOMs. * Updated upstream URL in manpages. -- Michael Hanke Wed, 12 Sep 2007 14:08:57 +0200 dicomnifti (2.28-1) unstable; urgency=low * New upstream release. Upstream switched from custom makefiles to CMake-based build system. * Converted NIfTI files now contain SPM5-like acquisition information. (Closes: #431591) * Bugfix: Wrong origin when converting sagital images (e.g. Siemens MPRAGE). (Closes: #431652) * Binaries are now build with -Wall -g -O2 by default (as it should be). * debian/rules honours DEB_BUILD_OPTIONS='noopt' and sets -O0 accordingly. * Removed dpatch build-dependency in favor of Git. * Fixed member init order in dicomInfo class. -- Michael Hanke Sun, 15 Jul 2007 20:59:07 +0200 dicomnifti (2.27-1) unstable; urgency=low * New upstream release. Fix image pixel location (half-pixel shift) to properly convert Siemens DICOMs. -- Michael Hanke Thu, 24 May 2007 06:45:08 +0200 dicomnifti (2.26.1-1) unstable; urgency=low * New upstream release. * Merged all non-Debian-specific patches with upstream. This also fixes the pending GCC 4.3 header issue that should have been fixed by the last upload, but wasn't as the included patch was disabled by mistake. (Closes: #417157) * Fixed bug: wrong header information (dimensions, etc) (Closes: #420019) -- Michael Hanke Wed, 25 Apr 2007 18:25:23 +0200 dicomnifti (2.25-2) unstable; urgency=low * Added patch to check for duplicate image series names. dinifti now modifies the series name and issues a warning instead of silently overwriting the file. * Added patch to add a --noact option to be able to quickly inspect the content of a DICOM directory without having to actually write the NIfTI files. * Documented the new behavior and options in the manpage. * Added patch to fix a missing header dependency which would result in a FTBFS with the coming GCC 4.3. Thanks to Martin Michlmayr for providing the patch. (Closes: #417157) -- Michael Hanke Thu, 5 Apr 2007 15:27:38 +0200 dicomnifti (2.25-1) unstable; urgency=low * New upstream release. Fixes a bug when converting MOSAIC images with a rectangular FOV. -- Michael Hanke Sat, 17 Mar 2007 07:47:01 +0100 dicomnifti (2.24-1) unstable; urgency=low * New upstream release. Fixes a problem when converting DICOMs from 3T GE scanners. -- Michael Hanke Thu, 22 Feb 2007 08:11:08 +0100 dicomnifti (2.23-1) unstable; urgency=low * New upstream release. Fixes a bug that caused dinifti to crash if not all DICOMs of an image series are available. * Merged most patches with upstream. Thanks to Valerio Luccio. * Added an additional space to the Homepage field in debian/control. * Updated debian/copyright (year in the copyright statement). -- Michael Hanke Wed, 21 Feb 2007 10:20:24 +0100 dicomnifti (2.22-2) unstable; urgency=low * Fixed a number of memory leaks. I'm grateful to Yaroslav Halchenko for pointing to a nasty STL-related bug. (Closes: #394834) * Build-depend on ctn-dev >> 3.0.6-9 to finally solve the datatype size issues on 64bit systems (see #387183). * Added upstream homepage to the package description. -- Michael Hanke Sun, 28 Jan 2007 19:24:44 +0100 dicomnifti (2.22-1) unstable; urgency=low * New upstream release. * Patches merged with upstream. -- Michael Hanke Thu, 5 Oct 2006 19:49:23 +0200 dicomnifti (2.21-3) unstable; urgency=low * Added --verbose option to enable a more verbose status output. This is mostly useful to associate dinifti warnings with certain image series, when converting directories containing multiple series. -- Michael Hanke Thu, 21 Sep 2006 19:50:56 +0200 dicomnifti (2.21-2) unstable; urgency=low * Added dependency to autotools-dev to get fresh copies of config.sub and config.guess. This fixes a FTBFS on AMD64. * Possible silent overwrite of converted files is noted in the manpage. -- Michael Hanke Mon, 4 Sep 2006 12:57:25 +0200 dicomnifti (2.21-1) unstable; urgency=low * New upstream release. -- Michael Hanke Tue, 29 Aug 2006 07:43:13 +0200 dicomnifti (2.20-1) unstable; urgency=low * New upstream release. * Added minimal manpage for dicomhead, enhanced manpage for dinifti. Both are forwarded to upstream and will become part of the next upstream release. -- Michael Hanke Mon, 28 Aug 2006 16:11:43 +0200 dicomnifti (2.11-1) unstable; urgency=low * Initial release. (Closes: #383563) -- Michael Hanke Wed, 16 Aug 2006 02:11:44 +0200 debian/rules0000755000000000000000000000052411421411373010244 0ustar #!/usr/bin/make -f # -*- makefile -*- # default CMake flags: # set manpage install dir to temp directory -- manpages will be installed # by dh_installman CMAKE_FLAGS = -DDINIFTI_MAN_DIR:PATH=../../tmp/manpages # one ring to rule them all ... %: dh $@ --buildsystem=cmake override_dh_auto_configure: dh_auto_configure -- $(CMAKE_FLAGS) debian/docs0000644000000000000000000000000710746156114010043 0ustar README debian/compat0000644000000000000000000000000210746156114010371 0ustar 5 debian/manpages0000644000000000000000000000003610746156114010710 0ustar man/dicomhead.1 man/dinifti.1 debian/watch0000644000000000000000000000010710746156114010222 0ustar version=3 http://cbi.nyu.edu/Downloads/DICOMNIfTI.([\d\.]+)\.tar\.gz debian/patches/0000755000000000000000000000000011515410535010615 5ustar debian/patches/unnecessary_linking0000644000000000000000000000065411421411373014614 0ustar --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -89,8 +89,7 @@ ADD_EXECUTABLE(dinifti src/dinifti.cc src/dicomInfo.cc src/niftiout.cc) TARGET_LINK_LIBRARIES( dinifti ${DINIFTI_CTN_LIB} ${DINIFTI_NIFTIIO_LIB} - ${DINIFTI_ZNZ_LIB} - z ) + ${DINIFTI_ZNZ_LIB}) # dicomhead ADD_EXECUTABLE(dicomhead src/dicomhead.cc src/dicomInfo.cc) debian/patches/series0000644000000000000000000000002411515410535012026 0ustar unnecessary_linking