new file mode 100644
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,588 @@
+SET(CMAKE_VERBOSE_MAKEFILE ON)
+
+# CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/config.h.cmake ${CMAKE_CURRENT_BINARY_DIR}/config.h )
+
+#ADD_SUBDIRECTORY( testdir )
+#ADD_SUBDIRECTORY( doc )
+
+# set the master INCLUDE directories
+INCLUDE_DIRECTORIES(
+   ${CMAKE_CURRENT_SOURCE_DIR}
+   ${CMAKE_SOURCE_DIR}/libsrc
+   ${CMAKE_SOURCE_DIR}/libsrc2
+   ${CMAKE_SOURCE_DIR}/volume_io/Include
+   )
+
+# some variables
+SET(minc1_LIB_SRCS
+   libsrc/ParseArgv.c
+   libsrc/dim_conversion.c
+   libsrc/image_conversion.c
+   libsrc/minc_convenience.c
+   libsrc/minc_error.c
+   libsrc/minc_globdef.c
+   libsrc/nd_loop.c
+   libsrc/netcdf_convenience.c
+   libsrc/time_stamp.c
+   libsrc/value_conversion.c
+   libsrc/voxel_loop.c
+   libsrc/hdf_convenience.c
+   libsrc/minc_compat.c
+   libsrc/minc_simple.c
+   )
+
+SET(minc2_LIB_SRCS
+   libsrc2/convert.c
+   libsrc2/datatype.c
+   libsrc2/dimension.c
+   libsrc2/free.c
+   libsrc2/grpattr.c
+   libsrc2/hyper.c
+   libsrc2/label.c
+   libsrc2/m2util.c
+   libsrc2/record.c
+   libsrc2/slice.c
+   libsrc2/valid.c
+   libsrc2/volprops.c
+   libsrc2/volume.c
+   )
+
+
+# build the main minc2 library
+ADD_LIBRARY(minc2 STATIC ${minc1_LIB_SRCS} ${minc2_LIB_SRCS})
+INSTALL(TARGETS minc2 DESTINATION lib)
+INSTALL(FILES libsrc/minc.h libsrc/ParseArgv.h 
+   libsrc/voxel_loop.h 
+   libsrc/nd_loop.h
+   libsrc/time_stamp.h
+   libsrc/minc_compat.h
+   volume_io/Include/volume_io.h
+   libsrc2/minc2.h
+   libsrc/minc_simple.h
+   DESTINATION include
+   )
+#SET_TARGET_PROPERTIES(minc2 PROPERTIES VERSION 4.2.0 SOVERSION 4 )
+
+
+# volume_io2
+SET(volume_io2_LIB_SRCS
+   volume_io/Geometry/colour.c
+   volume_io/Geometry/colour_def.c
+   volume_io/Geometry/gaussian.c
+   volume_io/Geometry/inverse.c
+   volume_io/Geometry/newton.c
+   volume_io/Geometry/points.c
+   volume_io/Geometry/splines.c
+   volume_io/Geometry/tensors.c
+   volume_io/Geometry/transforms.c
+   volume_io/MNI_formats/gen_xf_io.c
+   volume_io/MNI_formats/gen_xfs.c
+   volume_io/MNI_formats/grid_transforms.c
+   volume_io/MNI_formats/mni_io.c
+   volume_io/MNI_formats/tag_points.c
+   volume_io/MNI_formats/thin_plate_spline.c
+   volume_io/Prog_utils/alloc.c
+   volume_io/Prog_utils/alloc_check.c
+   volume_io/Prog_utils/arrays.c
+   volume_io/Prog_utils/files.c
+   volume_io/Prog_utils/print.c
+   volume_io/Prog_utils/progress.c
+   volume_io/Prog_utils/string.c
+   volume_io/Prog_utils/time.c
+   volume_io/Volumes/evaluate.c
+   volume_io/Volumes/get_hyperslab.c
+   volume_io/Volumes/input_free.c
+   volume_io/Volumes/input_mnc.c
+   volume_io/Volumes/input_volume.c
+   volume_io/Volumes/multidim_arrays.c
+   volume_io/Volumes/output_mnc.c
+   volume_io/Volumes/output_volume.c
+   volume_io/Volumes/set_hyperslab.c
+   volume_io/Volumes/volume_cache.c
+   volume_io/Volumes/volumes.c
+   )
+
+# build and install volume_io2 library
+ADD_LIBRARY(volume_io2 STATIC ${volume_io2_LIB_SRCS})
+INSTALL(TARGETS volume_io2 DESTINATION lib)
+INSTALL(FILES volume_io/Include/volume_io/alloc.h
+	volume_io/Include/volume_io/arrays.h 
+	volume_io/Include/volume_io/basic.h 
+	volume_io/Include/volume_io/def_math.h 
+	volume_io/Include/volume_io/files.h 
+	volume_io/Include/volume_io/geom_structs.h 
+	volume_io/Include/volume_io/geometry.h 
+	volume_io/Include/internal_volume_io.h 
+	volume_io/Include/volume_io/multidim.h 
+	volume_io/Include/volume_io/progress.h 
+	volume_io/Include/volume_io/string_funcs.h 
+	volume_io/Include/volume_io/system_dependent.h 
+	volume_io/Include/volume_io/transforms.h 
+	volume_io/Include/volume_io/vol_io_prototypes.h 
+	volume_io/Include/volume_io/volume.h 
+	volume_io/Include/volume_io/volume_cache.h
+   DESTINATION include/volume_io)
+
+#SET_TARGET_PROPERTIES(volume_io2 PROPERTIES VERSION 4.2.0 SOVERSION 4 )
+
+
+
+
+# 
+# ########### next target ###############
+# 
+# SET(acr_nema_STAT_SRCS
+#    conversion/Acr_nema/acr_io.c
+#    conversion/Acr_nema/dicom_client_routines.c
+#    conversion/Acr_nema/dicom_network.c
+#    conversion/Acr_nema/element.c
+#    conversion/Acr_nema/file_io.c
+#    conversion/Acr_nema/globals.c
+#    conversion/Acr_nema/group.c
+#    conversion/Acr_nema/message.c
+#    conversion/Acr_nema/value_repr.c
+#    )
+# 
+# ADD_LIBRARY(acr_nema STATIC ${acr_nema_STAT_SRCS})
+# 
+# 
+# ########### next target ###############
+# 
+# SET(voxeltoworld_SRCS
+#    progs/coordinates/voxeltoworld.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(voxeltoworld )
+# 
+# INSTALL( TARGETS voxeltoworld DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(worldtovoxel_SRCS
+#    progs/coordinates/worldtovoxel.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(worldtovoxel )
+# 
+# INSTALL( TARGETS worldtovoxel DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(minc_modify_header_SRCS
+#    progs/minc_modify_header/minc_modify_header.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(minc_modify_header )
+# 
+# INSTALL( TARGETS minc_modify_header DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(mincaverage_SRCS
+#    progs/mincaverage/mincaverage.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(mincaverage )
+# 
+# INSTALL( TARGETS mincaverage DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(minccalc_SRCS
+#    progs/minccalc/minccalc.c
+#    progs/minccalc/gram.y
+#    progs/minccalc/eval.c
+#    progs/minccalc/ident.c
+#    progs/minccalc/lex.l
+#    progs/minccalc/node.c
+#    progs/minccalc/optim.c
+#    progs/minccalc/scalar.c
+#    progs/minccalc/sym.c
+#    progs/minccalc/vector.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(minccalc )
+# 
+# INSTALL( TARGETS minccalc DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(mincconcat_SRCS
+#    progs/mincconcat/mincconcat.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(mincconcat )
+# 
+# INSTALL( TARGETS mincconcat DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(minccopy_SRCS
+#    progs/minccopy/minccopy.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(minccopy )
+# 
+# INSTALL( TARGETS minccopy DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(mincexpand_SRCS
+#    progs/mincexpand/mincexpand.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(mincexpand  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS mincexpand DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(mincextract_SRCS
+#    progs/mincextract/mincextract.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(mincextract  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS mincextract DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(mincgen_SRCS
+#    progs/mincgen/escapes.c
+#    progs/mincgen/genlib.c
+#    progs/mincgen/getfill.c
+#    progs/mincgen/init.c
+#    progs/mincgen/load.c
+#    progs/mincgen/main.c
+#    progs/mincgen/ncgentab.y
+#    progs/mincgen/ncgenyy.l
+#    )
+# 
+# TARGET_LINK_LIBRARIES(mincgen  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS mincgen DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(mincinfo_SRCS
+#    progs/mincinfo/mincinfo.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(mincinfo  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS mincinfo DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(minclookup_SRCS
+#    progs/minclookup/minclookup.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(minclookup  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS minclookup DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(mincmakescalar_SRCS
+#    progs/mincmakescalar/mincmakescalar.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(mincmakescalar  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS mincmakescalar DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(mincmakevector_SRCS
+#    progs/mincmakevector/mincmakevector.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(mincmakevector  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS mincmakevector DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(mincmath_SRCS
+#    progs/mincmath/mincmath.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(mincmath  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS mincmath DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(mincresample_SRCS
+#    progs/mincresample/mincresample.c
+#    progs/mincresample/resample_volumes.c
+#    progs/Proglib/convert_origin_to_start.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(mincresample  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS mincresample DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(mincreshape_SRCS
+#    progs/mincreshape/mincreshape.c
+#    progs/mincreshape/copy_data.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(mincreshape  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS mincreshape DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(mincstats_SRCS
+#    progs/mincstats/mincstats.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(mincstats  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS mincstats DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(minctoraw_SRCS
+#    progs/minctoraw/minctoraw.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(minctoraw  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS minctoraw DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(invert_raw_image_SRCS
+#    progs/mincview/invert_raw_image.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(invert_raw_image  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS invert_raw_image DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(mincwindow_SRCS
+#    progs/mincwindow/mincwindow.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(mincwindow  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS mincwindow DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(rawtominc_SRCS
+#    progs/rawtominc/rawtominc.c
+#    progs/Proglib/convert_origin_to_start.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(rawtominc  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS rawtominc DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(transformtags_SRCS
+#    progs/xfm/transformtags.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(transformtags  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS transformtags DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(xfmconcat_SRCS
+#    progs/xfm/xfmconcat.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(xfmconcat  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS xfmconcat DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(xfminvert_SRCS
+#    progs/xfm/xfminvert.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(xfminvert  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS xfminvert DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(mincconvert_SRCS
+#    progs/mincconvert/mincconvert.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(mincconvert  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS mincconvert DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(mincdump_SRCS
+#    progs/mincdump/mincdump.c
+#    progs/mincdump/vardata.c
+#    progs/mincdump/dumplib.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(mincdump  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS mincdump DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(ecattominc_SRCS
+#    conversion/ecattominc/ecattominc.c
+#    conversion/ecattominc/insertblood.c
+#    conversion/ecattominc/ecat_file.c
+#    conversion/ecattominc/machine_indep.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(ecattominc  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS ecattominc DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(minctoecat_SRCS
+#    conversion/minctoecat/minctoecat.c
+#    conversion/minctoecat/ecat_write.c
+#    conversion/minctoecat/machine_indep.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(minctoecat  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS minctoecat DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(mnc2nii_SRCS
+#    conversion/nifti1/mnc2nii.c
+#    conversion/nifti1/nifti1_io.c
+#    conversion/nifti1/znzlib.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(mnc2nii  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS mnc2nii DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(nii2mnc_SRCS
+#    conversion/nifti1/nii2mnc.c
+#    conversion/nifti1/nifti1_io.c
+#    conversion/nifti1/znzlib.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(nii2mnc  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS nii2mnc DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(upet2mnc_SRCS
+#    conversion/micropet/upet2mnc.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(upet2mnc  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS upet2mnc DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(dcm2mnc_SRCS
+#    conversion/dcm2mnc/dcm2mnc.c
+#    conversion/dcm2mnc/dicom_to_minc.c
+#    conversion/dcm2mnc/siemens_to_dicom.c
+#    conversion/dcm2mnc/dicom_read.c
+#    conversion/dcm2mnc/minc_file.c
+#    conversion/dcm2mnc/progress.c
+#    conversion/dcm2mnc/string_to_filename.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(dcm2mnc  ${QT_AND_KDECORE_LIBS} acr_nema )
+# 
+# INSTALL( TARGETS dcm2mnc DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(vff2mnc_SRCS
+#    conversion/vff2mnc/vff2mnc.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(vff2mnc  ${QT_AND_KDECORE_LIBS} )
+# 
+# INSTALL( TARGETS vff2mnc DESTINATION bin)
+# 
+# 
+# ########### next target ###############
+# 
+# SET(mincexample1_SRCS
+#    progs/mincexample/mincexample1.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(mincexample1  ${QT_AND_KDECORE_LIBS} )
+# 
+# 
+# ########### next target ###############
+# 
+# SET(mincexample2_SRCS
+#    progs/mincexample/mincexample2.c
+#    )
+# 
+# TARGET_LINK_LIBRARIES(mincexample2  ${QT_AND_KDECORE_LIBS} )
+# 
+# 
+# ########### install files ###############
+# 
+# INSTALL(FILES   DESTINATION /include/volume_io )
+# INSTALL(FILES   progs/xfm/xfmflip DESTINATION  )
+# INSTALL(FILES   progs/mincdiff/mincdiff  
+#                 progs/mincedit/mincedit  
+#                 progs/mincheader/mincheader  
+#                 progs/minchistory/minchistory  
+#                 progs/mincpik/mincpik  
+#                 progs/mincview/mincview DESTINATION  )
+# INSTALL(FILES   DESTINATION /include/acr_nema )