debian/0000775000000000000000000000000012272646330007175 5ustar debian/voxbo.links0000664000000000000000000000011211501145353011357 0ustar /etc/voxbo /usr/lib/voxbo/etc /usr/lib/voxbo/bin/vbview2 /usr/bin/vbview2 debian/copyright0000664000000000000000000000402611515642617011135 0ustar Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat Upstream-Name: Voxbo Upstream-Source: http://www.voxbo.org Files: * Copyright: Copyright (c) 1998-2011 by The VoxBo Development Team License: GPL-3+ On Debian systems the full text of the GPL-3 License can be found in the `/usr/share/common-licenses/GPL-3' file. Files: brainBrowser/br_util.cpp, Copyright: Copyright (c) 1998-2010 by Daniel Y. Kimberg License: GPL-3+ On Debian systems the full text of the GPL-3 License can be found in the `/usr/share/common-licenses/GPL-3' file. Files: lib/nifti11_ref.h Copyright: None License: Public domain This files is identical to nifti1.h as shipped by the libnifti1-dev package. The code has been placed into the public domain. The copyright mentioned in this files refer to an auxillary header (dbh.h) that is not shipped with Voxbo sources. Files: crunch/norm_brainwarp.cpp, crunch/norm_main.cpp, crunch/norm_utils.cpp Copyright: Copyright (c) 1996 John Ashburner MRCCU/FIL License: GPL-2+ These files have been derived from Matlab code that was shipped with SPM (GPL-licensed, http://www.fil.ion.ucl.ac.uk/spm/) On Debian systems the full text of the GPL-2 License can be found in the `/usr/share/common-licenses/GPL-2' file. Files: lib/statthreshold.*, munge/vbthreshcalc.cpp Copyright: Copyright (c) 2003 Keith J. Worsley License: other These files have been derived from Matlab code. The original license was: Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that this copyright notice appears in all copies. The author and McGill University make no representations about the suitability of this software for any purpose. It is provided "as is" without express or implied warranty. Files: debian/* Copyright: Copyright 2010, Michael Hanke License: GPL-3+ On Debian systems the full text of the GPL-3 License can be found in the `/usr/share/common-licenses/GPL-3' file. debian/README.Debian0000664000000000000000000000042311501145353011226 0ustar voxbo for Debian ---------------- VoxBo is installed under /usr/lib/voxbo. One may want to adjust the PATH setting to include the /usr/lib/voxbo/bin directory that contains all commandline tools. -- Michael Hanke Mon, 21 Jun 2010 11:18:23 -0500 debian/voxbo.install0000664000000000000000000000014111501145353011707 0ustar dist/etc/* etc/voxbo/ dist/elements usr/lib/voxbo/ debian/vbview2.desktop usr/share/applications debian/changelog0000664000000000000000000000272012272646330011050 0ustar voxbo (1.8.5~svn1246-1ubuntu2) trusty; urgency=low * Add missing Boost System Library to link, resolving FTBFS. * Fix format string literals. -- Daniel T Chen Thu, 30 Jan 2014 16:26:27 -0500 voxbo (1.8.5~svn1246-1ubuntu1) oneiric; urgency=low * debian/rules: disable --as-needed linker option, it doesn't work with GSL libraries (see debbugs #456898 for details). -- Ilya Barygin Sun, 03 Jul 2011 23:32:41 +0400 voxbo (1.8.5~svn1246-1) unstable; urgency=low * New upstream code. -- Michael Hanke Fri, 25 Feb 2011 13:23:31 -0500 voxbo (1.8.5~svn1241-1) unstable; urgency=low * New upstream code with a number of new manpages. * Merged Debian manpage of vbview2 with upstream version (patch submitted). -- Michael Hanke Wed, 19 Jan 2011 14:22:42 -0500 voxbo (1.8.5~svn1222-1) unstable; urgency=low * New upstream code. * Changed uploader email to mih@debian.org. * Add 'get-orig-source' target to debian/rules. * Bumped standards-version to 3.9.1, no changes necessary. * Install SPM8-related scripts and add matlab-spm8 to suggested packages. -- Michael Hanke Mon, 13 Dec 2010 09:40:31 -0500 voxbo (1.8.5~svn1172-1) unstable; urgency=low * Initial Debian packaging based on debhelper's "dh" and using the new source package format 3.0 (quilt). Closes: #579284. -- Michael Hanke Sun, 06 Jun 2010 11:33:11 -0400 debian/vbview2.10000664000000000000000000000200111501145353010625 0ustar .TH VOXBO "1" "June 2010" "VoxBo vbview2" "User Commands" .SH "NAME" vbview2 \- VoxBo's image viewer .SH "SYNOPSIS" .B vbview2 [\fI\fR [\fI\fR ... ]] ... .SH "DESCRIPTION" This is VoxBo's all-purpose image viewer. It can be used to display anatomical images, timeseries images and statistical maps. The viewer supports images in NIfTI format, as well as VoxBo's own data format. .SH "OPTIONS" .TP \fB\-m\fR load a mask image .TP \fB\-a\fR load an auxiliary volume .TP \fB\-s\fR load a statistical map .TP \fB\-h\fR show help .TP \fB\-v\fR show version .SH "BUGREPORTS" If you discover bugs please report them to the VoxBo mailing list at \fIvoxbo-general@voxbo.org\fR. .SH "AUTHORS" \fBVoxBo\fR was written by Daniel Kimberg, Dongbo Hu, Mjumbe Poe, Kosh Banerjee, Tom King, Geoff Aguirre and Eric Zarahn. .PP This manual page was written by Michael Hanke , for the Debian project (but may be used by others). .SH "SEE ALSO" \fBVoxBo website:\fR http://www.voxbo.org debian/voxbo.manpages0000664000000000000000000000000611515635000012032 0ustar man/* debian/patches/0000775000000000000000000000000012272646260010626 5ustar debian/patches/boost_libs_underlinkage.patch0000664000000000000000000004145712272644766016562 0ustar Index: voxbo-1.8.5~svn1246/lib/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/lib/Makefile 2014-01-30 16:56:08.179990695 -0500 +++ voxbo-1.8.5~svn1246/lib/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -6,7 +6,7 @@ CXXFLAGS+=$(PICFLAG) -LIBS =$(LIBDIRS) $(LIBPATHS) -lm -lvbglm -lvbprefs -lvbio -lvbutil -lz $(DLLIB) $(GSL_LIBS) +LIBS =$(LIBDIRS) $(LIBPATHS) -lm -lvbglm -lvbprefs -lvbio -lvbutil -lz -lboost_system $(DLLIB) $(GSL_LIBS) IOOBJECTS=vbio.o tes.o cube.o imageutils.o mat.o png.o vb_vector.o\ vbpreplib.o FFOBJECTS=vbff.o ff_cub.o ff_tes.o ff_ref.o ff_dicom3d.o ff_dicom4d.o dicom.o\ @@ -57,28 +57,28 @@ ranlib libvbio.a libvbio.so: $(IOOBJECTS) $(FFOBJECTS) libvbprefs.so libvbutil.so - g++ -shared -Wl,-soname,$@ -o $@ $(LDFLAGS) -L. -lc -lz -lgsl -lpng -lvbprefs -lvbutil $^ + g++ -shared -Wl,-soname,$@ -o $@ $(LDFLAGS) $^ -L. -lc -lz -lgsl -lpng -lvbprefs -lvbutil -lboost_system libvbutil.a: $(UTILOBJECTS) ar rc libvbutil.a $^ ranlib libvbutil.a libvbutil.so: $(UTILOBJECTS) - g++ -shared -Wl,-soname,$@ -o $@ $(LDFLAGS) -lc -lz $^ + g++ -shared -Wl,-soname,$@ -o $@ $(LDFLAGS) $^ -lboost_system -lc -lz libvbprefs.a: $(VBPOBJECTS) ar rc libvbprefs.a $^ ranlib libvbprefs.a libvbprefs.so: $(VBPOBJECTS) libvbutil.so - g++ -shared -Wl,-soname,$@ -o $@ $(LDFLAGS) -L. -lc -lvbutil $^ + g++ -shared -Wl,-soname,$@ -o $@ $(LDFLAGS) $^ -L. -lc -lvbutil -lboost_system libvbscripts.a: $(SCRIPTOBJECTS) ar rc libvbscripts.a $^ ranlib libvbscripts.a libvbscripts.so: $(SCRIPTOBJECTS) libvbprefs.so libvbutil.so - g++ -shared -Wl,-soname,$@ -o $@ $(LDFLAGS) -L. -lc -lvbprefs -lvbutil $^ + g++ -shared -Wl,-soname,$@ -o $@ $(LDFLAGS) $^ -L. -lc -lvbprefs -lvbutil -lboost_system libvbglm.a: $(GLMOBJECTS) ar rc libvbglm.a $^ @@ -86,14 +86,14 @@ libvbglm.so: $(GLMOBJECTS) libvbio.so libvbutil.so libvbprefs.so # g++ -shared -Wl,-soname,$@ -o $@ $(LDFLAGS) -L. -lc -lgsl -lvbio -lvbutil -lvbscripts -lvbprefs $^ - g++ -shared -Wl,-soname,$@ -o $@ $(LDFLAGS) -L. -lc -lgsl -lvbio -lvbutil -lvbprefs $^ + g++ -shared -Wl,-soname,$@ -o $@ $(LDFLAGS) $^ -L. -lc -lgsl -lvbio -lvbutil -lvbprefs -lboost_system libdbutil.a: $(DBOBJECTS) ar rc libdbutil.a $^ ranlib libdbutil.a libdbutil.so: $(DBOBJECTS) libvbio.so libvbutil.so - g++ -shared -Wl,-soname,$@ -o $@ $(LDFLAGS) -L. -lc -lvbio -lvbutil $^ + g++ -shared -Wl,-soname,$@ -o $@ $(LDFLAGS) $^ -L. -lc -lvbio -lvbutil -lboost_system # and now for the building blocks Index: voxbo-1.8.5~svn1246/fileformats/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/fileformats/Makefile 2014-01-30 16:56:08.255987205 -0500 +++ voxbo-1.8.5~svn1246/fileformats/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -6,7 +6,7 @@ SHAREDFLAG=-shared -LIBS=$(LDFLAGS) $(LIBDIRS) -lvbio -lvbutil -lvbprefs -lz -lpng -lgsl -lgslcblas +LIBS=$(LDFLAGS) $(LIBDIRS) -lvbio -lvbutil -lvbprefs -lz -lpng -lgsl -lgslcblas -lboost_system ALLBINS=dcmsplit dicominfo ffinfo vbrename analyzeinfo niftiinfo BINS=$(ALLBINS) Index: voxbo-1.8.5~svn1246/munge/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/munge/Makefile 2014-01-30 16:56:08.187990324 -0500 +++ voxbo-1.8.5~svn1246/munge/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -8,7 +8,7 @@ # miscellaneous flags and such -LIBS =$(LDFLAGS) $(LIBDIRS) $(LIBPATHS) -lvbglm -lvbprefs -lvbio -lvbutil -lz -lpng $(DLLIB) $(GSL_LIBS) +LIBS =$(LDFLAGS) $(LIBDIRS) $(LIBPATHS) -lvbglm -lvbprefs -lvbio -lvbutil -lz -lpng -lboost_system $(DLLIB) $(GSL_LIBS) CONVERTERS=tes2cub vb2cub vb2img vb2imgs vb2tes vb2vmp vbconv MUNGERS=vbmunge vbcmp vbshift vbsmooth vbmaskmunge vecsplit vbinterpolate vbthresh Index: voxbo-1.8.5~svn1246/brainBrowser/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/brainBrowser/Makefile 2014-01-30 16:56:08.039997106 -0500 +++ voxbo-1.8.5~svn1246/brainBrowser/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -10,7 +10,7 @@ OBJECTS=br_util.o main.o myDB.o HEADERS=br_util.h main.h myDB.h region.h region_relation.h searchBrain.h synonym.h -LIBS =$(LDFLAGS) $(LIBDIRS) $(QTLIBDIRS) $(QTLIBS) -lvbprefs -lvbglm -lvbio -lvbutil -lz $(DLLIB) -lgsl -lgslcblas +LIBS =$(LDFLAGS) $(LIBDIRS) $(QTLIBDIRS) $(QTLIBS) -lvbprefs -lvbglm -lvbio -lvbutil -lz $(DLLIB) -lgsl -lgslcblas -lboost_system ALLBINS=brainBrowser BINS=brainBrowser Index: voxbo-1.8.5~svn1246/client/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/client/Makefile 2014-01-30 16:56:08.099994379 -0500 +++ voxbo-1.8.5~svn1246/client/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -7,8 +7,8 @@ CXXFLAGS += -DQT3_SUPPORT $(QTINCDIRS) -I../vbview VBVIEW_OBJECTS=../vbview/vbview.o ../vbview/vbview_ts.o ../vbview/vbview_layers.o ../vbview/vbview_render.o ../vbview/vbview_io.o ../vbview/vbqt_masker.o ../vbview/vbqt_canvas.o ../vbview/vbqt_glmselect.o ../vbview/vbqt_scalewidget.o -XLIBS=$(LDFLAGS) $(LIBDIRS) $(QTLIBDIRS) $(VBVIEW_OBJECTS) $(QTLIBS) -lvbglm -lvbprefs -lvbio -lvbutil -lz -lm -lpng -ldl -lgnutls-extra -lgnutls -lgcrypt -lgpg-error -ldbutil -lgsl -lgslcblas -ldb_cxx -NOXLIBS=$(LDFLAGS) $(LIBDIRS) -lvbglm -lvbprefs -lvbio -lvbutil -lz -lm -lpng -ldl -lgnutls-extra -lgnutls -lgcrypt -lgpg-error -ldbutil -lgsl -lgslcblas -ldb_cxx -lpthread +XLIBS=$(LDFLAGS) $(LIBDIRS) $(QTLIBDIRS) $(VBVIEW_OBJECTS) $(QTLIBS) -lvbglm -lvbprefs -lvbio -lvbutil -lz -lm -lpng -ldl -lgnutls-extra -lgnutls -lgcrypt -lgpg-error -ldbutil -lgsl -lgslcblas -ldb_cxx -lboost_system +NOXLIBS=$(LDFLAGS) $(LIBDIRS) -lvbglm -lvbprefs -lvbio -lvbutil -lz -lm -lpng -ldl -lgnutls-extra -lgnutls -lgcrypt -lgpg-error -ldbutil -lgsl -lgslcblas -ldb_cxx -lpthread -lboost_system W_OBJECTS=dbqscorebox.o dbqlineedit.o dbqimage.o dbqcombo.o dbqtimedate.o dbqtextedit.o dbqstub.o dbview.o dbclient.o dbqbrain.o dbdialogs.o dbmainwindow.o Index: voxbo-1.8.5~svn1246/crunch/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/crunch/Makefile 2014-01-30 16:56:08.275986286 -0500 +++ voxbo-1.8.5~svn1246/crunch/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -23,7 +23,7 @@ INCDIRS += -I/usr/local/include/octave LIBDIRS += -L/usr/local/lib/octave -LIBS =$(LDFLAGS) $(LIBDIRS) -lm -lvbglm -lvbprefs -lvbio -lvbutil -lz -lpng $(DLLIB) $(GSL_LIBS) +LIBS =$(LDFLAGS) $(LIBDIRS) -lm -lvbglm -lvbprefs -lvbio -lvbutil -lz -lpng -lboost_system $(DLLIB) $(GSL_LIBS) OCTLIBS = $(LIBS) -loctave -lcruft $(FORTLIB) ALLBINS=vbmm2 vbmakeglm vbmakefilter #realign norm Index: voxbo-1.8.5~svn1246/dbutil/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/dbutil/Makefile 2014-01-30 16:56:07.936001854 -0500 +++ voxbo-1.8.5~svn1246/dbutil/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -4,7 +4,7 @@ -include ../make_vars.txt include ../make_stuff.txt -LIBS=$(LDFLAGS) $(LIBDIRS) -lm -ldbutil -lgnutls -lgnutls-extra -lgcrypt -lgpg-error -ldb_cxx -lvbprefs -lvbglm -lvbio -lvbutil -lgsl -lgslcblas -lz -lpng -ldl -lpthread +LIBS=$(LDFLAGS) $(LIBDIRS) -lm -ldbutil -lgnutls -lgnutls-extra -lgcrypt -lgpg-error -ldb_cxx -lvbprefs -lvbglm -lvbio -lvbutil -lgsl -lgslcblas -lz -lpng -ldl -lpthread -lboost_system ALLBINS=initDB initScoreValues # DYK: these binaries are not needed; this kind of functionality Index: voxbo-1.8.5~svn1246/gdscript/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/gdscript/Makefile 2014-01-30 16:56:08.011998350 -0500 +++ voxbo-1.8.5~svn1246/gdscript/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -13,7 +13,7 @@ GDS_OBJECTS = gds_main.o gds.o # miscellaneous flags and such -LIBS = $(LDFLAGS) $(LIBDIRS) $(DLLIB) -lm -lvbprefs -lvbglm -lvbio -lvbutil -lz -lpng $(GSL_LIBS) +LIBS = $(LDFLAGS) $(LIBDIRS) $(DLLIB) -lm -lvbprefs -lvbglm -lvbio -lvbutil -lz -lpng -lboost_system $(GSL_LIBS) ALLBINS=gds ifeq ($(VB_TARGET),all) Index: voxbo-1.8.5~svn1246/getput/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/getput/Makefile 2014-01-30 16:56:08.295985368 -0500 +++ voxbo-1.8.5~svn1246/getput/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -8,10 +8,10 @@ all: getdata putdata getdata: getdata.cpp time_series_avg.cpp $(VBLIBS) - ${CXX} -I../stand_alone ${CXXFLAGS} -Wall getdata.cpp time_series_avg.cpp $(LDFLAGS) -lvbio -lvbutil -lvbglm -lgsl -lgslcblas $(DLLIB) -o getdata + ${CXX} -I../stand_alone ${CXXFLAGS} -Wall getdata.cpp time_series_avg.cpp $(LDFLAGS) -lvbio -lvbutil -lvbglm -lgsl -lgslcblas -lboost_system $(DLLIB) -o getdata putdata: putdata.cpp $(VBLIBS) - ${CXX} ${CXXFLAGS} -Wall putdata.cpp $(LDFLAGS) -lvbio -lvbutil -lvbglm -lgsl -lgslcblas $(DLLIB) -o putdata + ${CXX} ${CXXFLAGS} -Wall putdata.cpp $(LDFLAGS) -lvbio -lvbutil -lvbglm -lgsl -lgslcblas -lboost_system $(DLLIB) -o putdata clean: rm -f /tmp/fifo getdata putdata *~ *.o *.exe Index: voxbo-1.8.5~svn1246/qtglm/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/qtglm/Makefile 2014-01-30 16:56:08.159991601 -0500 +++ voxbo-1.8.5~svn1246/qtglm/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -20,7 +20,7 @@ PERMGEN_OBJECTS= vbpermgen.o # miscellaneous flags and such -LIBS=$(LDFLAGS) $(LIBDIRS) $(QTLIBDIRS) $(QTLIBS) -lz -lvbglm -lvbprefs -lvbio -lvbutil -lz $(GSL_LIBS) $(DLLIB) +LIBS=$(LDFLAGS) $(LIBDIRS) $(QTLIBDIRS) $(QTLIBS) -lz -lvbglm -lvbprefs -lvbio -lvbutil -lz -lboost_system $(GSL_LIBS) $(DLLIB) ALLBINS= glm gdw vecview vbpermgen vbtcalc OSXTRA=glm.app glm.dmg gdw.app gdw.dmg vecview.app vecview.dmg vbpermgen.app vbpermgen.dmg vbtcalc.app vbtcalc.dmg Index: voxbo-1.8.5~svn1246/qtvlsm/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/qtvlsm/Makefile 2014-01-30 16:56:08.219988858 -0500 +++ voxbo-1.8.5~svn1246/qtvlsm/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -8,7 +8,7 @@ PERMUTATION_OBJECTS=../stand_alone/perm.o ../stand_alone/utils.o ../stand_alone/time_series_avg.o ../stand_alone/koshutil.o OBJECTS=vbvlsm.o rsrc.o $(PERMUTATION_OBJECTS) -LIBS = $(LDFLAGS) $(LIBDIRS) $(QTLIBDIRS) $(QTLIBS) -Xlinker -lvbglm -lvbprefs -lvbio -lvbutil -lz $(DLLIB) -lgsl -lgslcblas +LIBS = $(LDFLAGS) $(LIBDIRS) $(QTLIBDIRS) $(QTLIBS) -Xlinker -lvbglm -lvbprefs -lvbio -lvbutil -lz -lboost_system $(DLLIB) -lgsl -lgslcblas ALLBINS=vbvlsm ifeq ($(VB_TARGET),all) Index: voxbo-1.8.5~svn1246/resample/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/resample/Makefile 2014-01-30 16:56:08.047996750 -0500 +++ voxbo-1.8.5~svn1246/resample/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -11,7 +11,7 @@ # miscellaneous flags and such -LIBS = $(LDFLAGS) $(LIBDIRS) -lm -lvbprefs -lvbio -lvbutil -lz -lpng $(DLLIB) $(GSL_LIBS) +LIBS = $(LDFLAGS) $(LIBDIRS) -lm -lvbprefs -lvbio -lvbutil -lz -lpng -lboost_system $(DLLIB) $(GSL_LIBS) # resample is in all packages BINS=resample Index: voxbo-1.8.5~svn1246/scheduler/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/scheduler/Makefile 2014-01-30 16:56:08.115993619 -0500 +++ voxbo-1.8.5~svn1246/scheduler/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -4,7 +4,7 @@ -include ../make_vars.txt include ../make_stuff.txt -LIBS=$(LDFLAGS) $(LIBDIRS) -lvbprefs -lvbutil -lz +LIBS=$(LDFLAGS) $(LIBDIRS) -lvbprefs -lvbutil -lz -lboost_system ALLBINS=voxbo vbsrvd voxq vbq vq ifeq ($(VB_TARGET),all) Index: voxbo-1.8.5~svn1246/server/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/server/Makefile 2014-01-30 16:56:08.247987571 -0500 +++ voxbo-1.8.5~svn1246/server/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -4,7 +4,7 @@ -include ../make_vars.txt include ../make_stuff.txt -LIBS=$(LDFLAGS) $(LIBDIRS) $(VBVIEW_OBJECTS) -lvbprefs -lvbglm -lvbio -lvbutil -lz -lm -lpng -ldl -lgnutls-extra -lgnutls -lgcrypt -lgpg-error -ldbutil -lgsl -lgslcblas -ldb_cxx -lpthread +LIBS=$(LDFLAGS) $(LIBDIRS) $(VBVIEW_OBJECTS) -lvbprefs -lvbglm -lvbio -lvbutil -lz -lm -lpng -ldl -lgnutls-extra -lgnutls -lgcrypt -lgpg-error -ldbutil -lgsl -lgslcblas -ldb_cxx -lpthread -lboost_system ALLBINS=server Index: voxbo-1.8.5~svn1246/stand_alone/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/stand_alone/Makefile 2014-01-30 16:56:08.023997898 -0500 +++ voxbo-1.8.5~svn1246/stand_alone/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -13,7 +13,7 @@ REGRESSION_OBJECTS=regression.o utils.o koshutil.o PERMUTATION_OBJECTS=perm.o utils.o time_series_avg.o koshutil.o -LIBS=$(LDFLAGS) $(LIBDIRS) -lvbglm -lvbprefs -lvbio -lvbutil -lz -lpng $(GSL_LIBS) $(DLLIB) +LIBS=$(LDFLAGS) $(LIBDIRS) -lvbglm -lvbprefs -lvbio -lvbutil -lz -lpng -lboost_system $(GSL_LIBS) $(DLLIB) ALLBINS= calcgs calcps sliceacq tesplit tesjoin makematkg makematk\ comptraces permstep vbregress vbpermmat Index: voxbo-1.8.5~svn1246/stats/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/stats/Makefile 2014-01-30 16:56:07.991999349 -0500 +++ voxbo-1.8.5~svn1246/stats/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -8,7 +8,7 @@ # miscellaneous flags and such -LIBS = $(LDFLAGS) $(LIBDIRS) -lm -lvbprefs -lvbglm -lvbio -lvbutil -lz -lpng $(DLLIB) $(GSL_LIBS) +LIBS = $(LDFLAGS) $(LIBDIRS) -lm -lvbprefs -lvbglm -lvbio -lvbutil -lz -lpng -lboost_system $(DLLIB) $(GSL_LIBS) ALLBINS=vbvolregress vbmakeregress vbstatmap vbdumpstats glminfo vbperminfo ALLBINS+=vbxts vbtmap vbmakeresid vbfdr vbpermvec vbscoregen vbmap Index: voxbo-1.8.5~svn1246/utils/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/utils/Makefile 2014-01-30 16:56:08.227988490 -0500 +++ voxbo-1.8.5~svn1246/utils/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -7,7 +7,7 @@ # Some variables MYLIBVOXBO=../lib -LIBS = $(LDFLAGS) $(LIBDIRS) -lvbglm -lvbprefs -lvbio -lvbutil -lz -lpng $(DLLIB) $(GSL_LIBS) +LIBS = $(LDFLAGS) $(LIBDIRS) -lvbglm -lvbprefs -lvbio -lvbutil -lz -lpng -lboost_system $(DLLIB) $(GSL_LIBS) ALLBINS=vbfit vbcfx txt2num gcheck sortmvpm ifeq ($(VB_TARGET),all) Index: voxbo-1.8.5~svn1246/vbsequence/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/vbsequence/Makefile 2014-01-30 16:56:08.207989409 -0500 +++ voxbo-1.8.5~svn1246/vbsequence/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -15,7 +15,7 @@ moc_vbjobtypelistmodel.o moc_vbsequenceview.o moc_vbsequencescene.o \ moc_vbsequenceitem.o moc_vbdatasetwidget.o XLIBS=$(QTLIBDIRS) -LIBS=$(LDFLAGS) $(LIBDIRS) $(XLIBS) -lvbprefs -lvbio -lvbutil -lvbscripts -lz -lpng $(DLLIB) $(GSL_LIBS) +LIBS=$(LDFLAGS) $(LIBDIRS) $(XLIBS) -lvbprefs -lvbio -lvbutil -lvbscripts -lz -lpng -lboost_system $(DLLIB) $(GSL_LIBS) ALLBINS=vbsequence submit_sequence print_dataset display_dataset Index: voxbo-1.8.5~svn1246/vbview/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/vbview/Makefile 2014-01-30 16:56:08.267986653 -0500 +++ voxbo-1.8.5~svn1246/vbview/Makefile 2014-01-30 16:56:17.247555232 -0500 @@ -11,7 +11,7 @@ VBVIEW_SUBOBJECTS=vbview.o vbview_ts.o vbview_layers.o vbview_render.o vbview_io.o vbqt_masker.o vbqt_canvas.o vbqt_glmselect.o vbqt_scalewidget.o rsrc.o VBVIEW_OBJECTS=vbviewmain.o $(VBVIEW_SUBOBJECTS) -LIBS=$(LDFLAGS) $(LIBDIRS) $(QTLIBDIRS) -L../vbwidgets $(QTLIBS) -lvbglm -lvbprefs -lvbio -lvbutil -lz $(DLLIB) -lgsl -lgslcblas +LIBS=$(LDFLAGS) $(LIBDIRS) $(QTLIBDIRS) -L../vbwidgets $(QTLIBS) -lvbglm -lvbprefs -lvbio -lvbutil -lz -lboost_system $(DLLIB) -lgsl -lgslcblas # right now all three programs are in all packages, so we just # conditionalize on ARCH Index: voxbo-1.8.5~svn1246/vbwidgets/Makefile =================================================================== --- voxbo-1.8.5~svn1246.orig/vbwidgets/Makefile 2014-01-30 16:56:07.928002261 -0500 +++ voxbo-1.8.5~svn1246/vbwidgets/Makefile 2014-01-31 02:00:02.817845721 -0500 @@ -13,7 +13,7 @@ # miscellaneous flags and such XLIBS = $(QTLIBDIRS) -lX11 -lXext -lpthread -LIBS = $(LDFLAGS) $(LIBDIRS) $(XLIBS) -Xlinker -lvbprefs -lvbio -lvbutil -lz $(DLLIB) -lvbglm -lgsl -lgslcblas +LIBS = $(LDFLAGS) $(LIBDIRS) $(XLIBS) -Xlinker -lvbprefs -lvbio -lvbutil -lz $(DLLIB) -lvbglm -lgsl -lgslcblas -lboost_system ifdef VB_SHARED TARGETS=libvbwidgets.so @@ -47,7 +47,7 @@ ranlib libvbwidgets.a libvbwidgets.so: $(VBWIDGET_OBJECTS) - g++ -shared -Wl,-soname,$@ $(LDFLAGS) -o $@ -lc $^ -L../lib -lvbio -lvbutil -lvbprefs -lvbglm -lQtCore -lQt3Support -lQtGui -lgsl + g++ -shared -Wl,-soname,$@ $(LDFLAGS) -o $@ -lc $^ -L../lib -lvbio -lvbutil -lvbprefs -lvbglm -lQtCore -lQt3Support -lQtGui -lgsl -lboost_system moc_%.cpp : %.h $(MOC) $< -o $@ debian/patches/no_qtimageformats_linking0000664000000000000000000000037211515631744016005 0ustar --- a/make_stuff.txt +++ b/make_stuff.txt @@ -96,7 +96,7 @@ endif ifdef VB_SHARED - QTLIBS+=-lqgif -lqjpeg -lqtiff + #QTLIBS+=-lqgif -lqjpeg -lqtiff QTLIBDIRS+=-L$(QTDIR)/plugins/imageformats -L$(QTDIR)/lib/qt4/plugins/imageformats endif debian/patches/manpages0000664000000000000000000000073411515634742012351 0ustar --- a/man/vbview2.1 +++ b/man/vbview2.1 @@ -13,6 +13,22 @@ projections or surface renderings. It allows an arbitrary number of layers and graphs time series data. .SH OPTIONS +.TP +\fB\-m\fR +load a mask image +.TP +\fB\-a\fR +load an auxiliary volume +.TP +\fB\-s\fR +load a statistical map +.TP +\fB\-h\fR +show help +.TP +\fB\-v\fR +show version +.P To get a complete list of available flags, run the program with the -h argument. .SH AVAILABILITY debian/patches/series0000664000000000000000000000013512272646036012043 0ustar no_qtimageformats_linking manpages boost_libs_underlinkage.patch format-string-literal.patch debian/patches/format-string-literal.patch0000664000000000000000000000423512272646260016101 0ustar Index: voxbo-1.8.5~svn1246/gdscript/gds.cpp =================================================================== --- voxbo-1.8.5~svn1246.orig/gdscript/gds.cpp 2011-02-25 13:25:15.000000000 -0500 +++ voxbo-1.8.5~svn1246/gdscript/gds.cpp 2014-01-31 02:10:37.425335866 -0500 @@ -4403,7 +4403,7 @@ fprintf(condLabFile, ";VB98\n"); fprintf(condLabFile, ";TXT1\n\n"); for (size_t i = 0; i < condKey.size(); i++) { - fprintf(condLabFile, condKey(i)); + fprintf(condLabFile, "%s", condKey(i)); fprintf(condLabFile, "\n"); } @@ -4422,14 +4422,14 @@ fprintf(covFile, ";REF1\n"); fprintf(covFile, ";\n"); fprintf(covFile, ";; Single covariate from G matrix\n"); - fprintf(covFile, myComments.c_str()); + fprintf(covFile, "%s", myComments.c_str()); fprintf(covFile, ";\n"); char numLine[100]; VB_Vector downVec = *downSampling(&(covList[covID].varvec), TR / tmpResolve); for (unsigned i = 0; i < downVec.getLength(); i++) { sprintf(numLine, "%f\n", downVec.getElement(i)); - fprintf(covFile, numLine); + fprintf(covFile, "%s", numLine); } fclose(covFile); Index: voxbo-1.8.5~svn1246/qtglm/gdw.cpp =================================================================== --- voxbo-1.8.5~svn1246.orig/qtglm/gdw.cpp 2011-02-25 13:25:15.000000000 -0500 +++ voxbo-1.8.5~svn1246/qtglm/gdw.cpp 2014-01-31 02:11:40.606381255 -0500 @@ -4171,7 +4171,7 @@ const char *tmpString; for (unsigned i = 0; i < keyList->count(); i++) { tmpString = keyList->text(i); - fprintf(condLabFile, tmpString); + fprintf(condLabFile, "%s", tmpString); fprintf(condLabFile, "\n"); } @@ -4239,14 +4239,14 @@ fprintf(covFile, ";REF1\n"); fprintf(covFile, ";\n"); fprintf(covFile, ";; Single covariate from G matrix\n"); - fprintf(covFile, selLine.ascii()); + fprintf(covFile, "%s", selLine.ascii()); fprintf(covFile, ";\n"); char numLine[100]; VB_Vector *downVec = downSampling(covList[selIndex], TR / tmpResolve); for (unsigned i = 0; i < downVec->getLength(); i++) { sprintf(numLine, "%f\n", downVec->getElement(i)); - fprintf(covFile, numLine); + fprintf(covFile, "%s", numLine); } fclose(covFile); debian/voxbo.menu0000664000000000000000000000031711501145353011212 0ustar ?package(voxbo): \ needs="X11" \ section="Applications/Science/Medicine" \ title="VBView2" \ longtitle="VoxBo Image Viewer for (f)MRI" \ command="/usr/bin/vbview2" \ hints="MRI,fMRI" debian/control0000664000000000000000000000230212272542652010577 0ustar Source: voxbo Priority: extra Maintainer: Ubuntu Developers XSBC-Original-Maintainer: NeuroDebian Team Uploaders: Michael Hanke , Yaroslav Halchenko Build-Depends: debhelper (>= 7.0.50~), python, zlib1g-dev, libboost-dev, libboost-thread-dev, libgsl0-dev, libpng12-dev | libpng-dev, libqt4-dev, libxi-dev, libxrender-dev, libfontconfig1-dev | libfontconfig-dev Standards-Version: 3.9.1 Section: science Homepage: http://www.voxbo.org XS-DM-Upload-Allowed: yes Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/voxbo.git Vcs-Git: git://git.debian.org/git/pkg-exppsy/voxbo.git Package: voxbo Section: science Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: mni-colin27-nifti, matlab-spm8 Description: processing, statistical analysis, and display of brain imaging data This is a toolkit for analysis of functional neuroimaging (chiefly fMRI) experiments and voxel-based lesion-behavior mapping. VoxBo supports the modified GLM (for autocorrelated data), as well as the standard GLM for non-autocorrelated data. The toolkit is designed to be interoperable with AFNI, FSL, SPM and others. debian/source/0000775000000000000000000000000011501145353010466 5ustar debian/source/format0000664000000000000000000000001411501145353011674 0ustar 3.0 (quilt) debian/vbview2.desktop0000664000000000000000000000033611501145353012147 0ustar [Desktop Entry] Encoding=UTF-8 GenericName=VoxBo Image Viewer Name=VBView2 Exec=vbview2 %F TryExec=vbview2 Type=Application Terminal=false Categories=Education;Graphics;Science;DataVisualization;MedicalSoftware;Qt;Viewer; debian/compat0000664000000000000000000000000211501145353010364 0ustar 7 debian/rules0000775000000000000000000000276512272542642010270 0ustar #!/usr/bin/make -f # -*- makefile -*- srcpkg = $(shell LC_ALL=C dpkg-parsechangelog | grep '^Source:' | cut -d ' ' -f 2,2) upstreamver = $(shell LC_ALL=C dpkg-parsechangelog | grep '^Version:' | cut -d ' ' -f 2,2 | cut -d '-' -f 1,1 ) export CXXFLAGS += -Wall export LDFLAGS += -Wl,--no-undefined -Wl,-rpath=/usr/lib/voxbo/lib -Wl,--no-as-needed # one ring to rule them all ... %: dh $@ override_dh_auto_configure: ./configure.py -s -p neurodebian override_dh_auto_build: $(MAKE) QTDIR=/usr \ QTBASEINCDIR=/usr/include/qt4 \ MOC=/usr/bin/moc-qt4 \ VB_SHARED=1 override_dh_auto_install: $(MAKE) install VB_PREFIX=$(CURDIR)/debian/voxbo/usr/lib/voxbo install -d $(CURDIR)/debian/voxbo/usr/lib/voxbo/lib install -t $(CURDIR)/debian/voxbo/usr/lib/voxbo/lib $(shell find . -name '*.so') # cleanup -rm $(CURDIR)/debian/voxbo/usr/lib/voxbo/bin/vbinstall # perm fixes chmod +x $(CURDIR)/debian/voxbo/usr/lib/voxbo/bin/spm8* override_dh_clean: $(MAKE) distclean dh_clean override_dh_shlibdeps: dh_shlibdeps -l $(CURDIR)/debian/voxbo/usr/lib/voxbo/lib override_dh_install: dh_install # remove obsolete license file (voxbo doesn't ship this template) but it # comes from the mni-colin27-nifti package -rm debian/voxbo/usr/lib/voxbo/elements/templates/ch2_license.txt # make orig tarball from repository content get-orig-source: # orig tarball, turn directory into something nicer git archive --format=tar --prefix=$(srcpkg)-$(upstreamver)/ HEAD | \ gzip -9 > $(srcpkg)_$(upstreamver).orig.tar.gz