Hi Sol, 6.0 is built with qt 4.7, and the freesurfer development branch currently uses qt 4.8.5
best, Andrew > On Nov 27, 2017, at 5:32 PM, Sol Jerome <s...@utdallas.edu> wrote: > > Andrew, > > Thanks, this helped me get past the error I was receiving. I am now > trying to determine exactly which QT libraries are required to > successfully complete compilation. I've tried both qt5-qtbase-devel as > well as qt-devel. Here are the resulting errors from each: > > > qt5-qtbase-devel: > > main.cpp:1:30: fatal error: QtGui/QApplication: No such file or directory > #include <QtGui/QApplication> > ^ > compilation terminated. > make[3]: *** [nmovie_qt-main.o] Error 1 > make[3]: *** Waiting for unfinished jobs.... > make[3]: Leaving directory `/builddir/build/BUILD/freesurfer-6.0.0/nmovie_qt' > make[2]: Leaving directory `/builddir/build/BUILD/freesurfer-6.0.0/nmovie_qt' > make[2]: *** [all] Error 2 > make[1]: Leaving directory `/builddir/build/BUILD/freesurfer-6.0.0' > make[1]: *** [all-recursive] Error 1 > make: *** [all] Error 2 > > > > qt-devel: > > make[3]: *** [freeview-moc_Cursor2D.o] Error 1 > make[3]: *** Waiting for unfinished jobs.... > make[3]: *** [freeview-moc_Cursor3D.o] Error 1 > In file included from GenericRenderView.h:27:0, > from moc_GenericRenderView.cpp:9: > QVTKWidget.h:92:42: error: 'Qt::WFlags' has not been declared > QVTKWidget(QWidget* parent = NULL, Qt::WFlags f = 0); > ^ > In file included from moc_GenericRenderView.cpp:9:0: > GenericRenderView.h:55:49: error: 'Qt::WFlags' has not been declared > GenericRenderView(QWidget* parent = NULL, Qt::WFlags f = 0); > ^ > make[3]: *** [freeview-moc_GenericRenderView.o] Error 1 > make[3]: Leaving directory `/builddir/build/BUILD/freesurfer-6.0.0/freeview' > make[2]: *** [all] Error 2 > make[2]: Leaving directory `/builddir/build/BUILD/freesurfer-6.0.0/freeview' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/builddir/build/BUILD/freesurfer-6.0.0' > make: *** [all] Error 2 > > > > Thanks, > Sol > > * Oct 05, 2017, at 19:54:55 PM, Hoopes, Andrew <ahoo...@mgh.harvard.edu> > wrote: >> It looks like you’re missing the hexdump program xxd, which converts the >> help text to a header file. I believe it’s found in the vim-common package: >> yum install vim-common >> >> Andrew >> >> >> On Oct 5, 2017, at 1:42 PM, Sol Jerome >> <s...@utdallas.edu<mailto:s...@utdallas.edu>> wrote: >> >> The header file does not exist. >> >> Here is the output from `make`: >> >> # make >> make: *** No rule to make target `lta_convert.help.xml.h', needed by `all'. >> Stop. >> >> Here is the content of the Makefile: >> >> # Makefile.in generated by automake 1.13.4 from Makefile.am. >> # lta_convert/Makefile. Generated from Makefile.in by configure. >> >> # Copyright (C) 1994-2013 Free Software Foundation, Inc. >> >> # This Makefile.in is free software; the Free Software Foundation >> # gives unlimited permission to copy and/or distribute it, >> # with or without modifications, as long as this notice is preserved. >> >> # This program is distributed in the hope that it will be useful, >> # but WITHOUT ANY WARRANTY, to the extent permitted by law; without >> # even the implied warranty of MERCHANTABILITY or FITNESS FOR A >> # PARTICULAR PURPOSE. >> >> >> >> >> >> am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)' >> am__make_running_with_option = \ >> case $${target_option-} in \ >> ?) ;; \ >> *) echo "am__make_running_with_option: internal error: invalid" \ >> "target option '$${target_option-}' specified" >&2; \ >> exit 1;; \ >> esac; \ >> has_opt=no; \ >> sane_makeflags=$$MAKEFLAGS; \ >> if $(am__is_gnu_make); then \ >> sane_makeflags=$$MFLAGS; \ >> else \ >> case $$MAKEFLAGS in \ >> *\\[\ \ ]*) \ >> bs=\\; 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autoconf >> AUTOHEADER = ${SHELL} /builddir/build/BUILD/freesurfer-6.0.0/config/missing >> autoheader >> AUTOMAKE = ${SHELL} /builddir/build/BUILD/freesurfer-6.0.0/config/missing >> automake-1.13 >> AWK = gawk >> BLT_CFLAGS = >> BLT_LIBS = >> BOOST_CFLAGS = >> BOOST_DIR = >> BOOST_LIB = >> BOOST_LIBS = >> BOOST_PO_LIB = >> BYTEORDER = 1234 >> CC = gcc >> CCDEPMODE = depmode=none >> CCLD = g++ >> CFLAGS = -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions >> -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches >> -m64 -mtune=generic >> CPP = gcc -E >> CPPFLAGS = -g -O3 -msse2 -mfpmath=sse -Wall -DUSE_SSE_MATHFUN -fopenmp >> -DHAVE_OPENMP -m64 -DLinux -DANSI >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/1.5/include >> CPPUNIT_CFLAGS = >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/cppunit/current/include >> CPPUNIT_DIR = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/cppunit/current >> CPPUNIT_LIB = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/cppunit/current/lib >> CPPUNIT_LIBS = >> -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/cppunit/current/lib >> CPUCAPS = model name : Intel(R) Xeon(R) CPU E5-2440 0 @ 2.40GHz >> CPUTYPE = intel_haswell >> CUDA_CFLAGS = >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/CUDA/current/include >> CUDA_DIR = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/CUDA/current >> CUDA_LIBS = >> -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/CUDA/current/lib64 >> -lcudart >> CXX = g++ >> CXXCPP = g++ -E >> CXXDEPMODE = depmode=none >> CXXFLAGS = -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions >> -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches >> -m64 -mtune=generic >> CYGPATH_W = echo >> DEFS = -DHAVE_CONFIG_H >> DEPDIR = .deps >> DYNAMIC_LIB_EXT = .so >> ECHO = echo >> ECHO_C = >> ECHO_N = -n >> ECHO_T = >> EGREP = /usr/bin/grep -E >> EXEEXT = >> EXPAT_CFLAGS = >> EXPAT_LIBS = >> F77 = gfortran >> FCLIBS = >> FFLAGS = -g -O3 -msse2 -mfpmath=sse >> FLTK_CXXFLAGS = >> FLTK_DIR = >> FLTK_LDFLAGS = >> FLTK_LIB = >> FLTK_LIBS = >> GDCM_CFLAGS = >> GDCM_DIR = >> GDCM_LIB = >> GDCM_LIBS = >> GLU_CFLAGS = >> GLU_LIBS = -lGLU -lGL -L/lib64 -lX11 -lm >> GL_CFLAGS = >> GL_LIBS = -lGL -L/lib64 -lX11 -lm >> GREP = /usr/bin/grep >> GTS_CFLAGS = >> GTS_DIR = >> GTS_LIBS = >> HAS_GZIP = 1 >> HAS_ZCAT = 1 >> HAVE_OPENGL = -DHAVE_OPENGL >> INSTALL = /usr/bin/install -c >> INSTALL_DATA = ${INSTALL} -m 644 >> INSTALL_PROGRAM = ${INSTALL} >> INSTALL_SCRIPT = ${INSTALL} >> INSTALL_STRIP_PROGRAM = $(install_sh) -c -s >> ITK_CFLAGS = >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/Algorithms >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/BasicFilters >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/Common >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/IO >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/Numerics >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/Numerics/Statistics >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/Review >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/Review/Statistics >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/SpatialObject >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/include/InsightToolkit/Utilities >> ITK_DIR = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current >> ITK_LIB = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit >> ITK_LIBS = >> -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit >> JPEG_CFLAGS = >> JPEG_LIBS = >> KWWIDGETS_CFLAGS = >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/KWWidgets/current/include/KWWidgets >> KWWIDGETS_CXXFLAGS = >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/KWWidgets/current/include/KWWidgets >> KWWIDGETS_DIR = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/KWWidgets/current >> KWWIDGETS_LIBS = >> -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/KWWidgets/current/lib/KWWidgets >> LATEX = >> LDFLAGS = >> -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/lib >> -L/usr/lib64 -L/usr/X11R6/lib64 -Wl,-z,relro -fopenmp >> -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/1.5/lib >> -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vxl/current/lib >> >> -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit >> LDFLAGS_TCL = >> -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/tcltktixblt/current/lib >> LIBDIRS_MGH = utils rgb unix dicom hipsstubs >> LIBOBJS = >> LIBS = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKIO.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKAlgorithms.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKCommon.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNumerics.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKMetaIO.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKniftiio.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNrrdIO.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkpng.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitksys.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitktiff.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkv3p_netlib.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkzlib.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkgdcm.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkopenjpeg.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg8.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg12.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg16.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKDICOMParser.a >> /usr/lib64/libuuid.so -lz -lm -lcrypt -ldl -lpthread /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/current/lib/libvolume_io.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/current/lib/libminc.a /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/current/lib/libnetcdf.a -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib >> LIBS_CUDA_MGH = utils/libutils_cuda.a fsgdf/libfsgdf.a rgb/librgb.a >> unix/libunix.a dicom/libdicom.a hipsstubs/libhipsstubs.a log/liblog.a >> xml2/libxml2.a jpeg/libjpeg.a tiff/libtiff.a expat/libexpat.a >> LIBS_GDCM = >> LIBS_ICC = >> LIBS_ITK = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKIO.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKAlgorithms.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKCommon.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNumerics.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKMetaIO.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKniftiio.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNrrdIO.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkpng.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitksys.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitktiff.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkv3p_netlib.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkzlib.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkgdcm.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkopenjpeg.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg8.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg12.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg16.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKDICOMParser.a >> /usr/lib64/libuuid.so >> LIBS_MGH = utils/libutils.a fsgdf/libfsgdf.a rgb/librgb.a >> unix/libunix.a dicom/libdicom.a hipsstubs/libhipsstubs.a log/liblog.a >> xml2/libxml2.a jpeg/libjpeg.a tiff/libtiff.a expat/libexpat.a >> LIBS_MNI = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/current/lib/libvolume_io.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/current/lib/libminc.a >> >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/current/lib/libnetcdf.a >> LIBS_NIFTI = >> LIBS_OPEN64 = >> LIBS_OPENGL = -lGLU -lGL -L/lib64 -lX11 -lm >> LIBS_TCL = -lBLT -ltix8.1.8.4 -ltk8.4 -ltcl8.4 >> LIBS_TCL_OPENGL = -lBLT -ltix8.1.8.4 -ltk8.4 -ltcl8.4 -lGLU -lGL -L/lib64 >> -lX11 -lm >> LIBS_VXL = -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib >> LIBS_XAWPLUS = -lXt -lXpm -lXawPlus >> LIBTOOL = $(SHELL) $(top_builddir)/libtool >> LIB_BLAS = /usr/lib64/libblas.a >> LIB_BLT = -lBLT >> LIB_BLT_JPEG = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/tiffjpegglut/current/lib/libjpeg.a >> LIB_CRYPT = -lcrypt >> LIB_CUDA = >> LIB_EXPAT = >> LIB_G2C_A = >> LIB_GFORTRAN = -lgfortran >> LIB_JPEG = >> LIB_LAPACK = /usr/lib64/liblapack.a >> LIB_NETCDF = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/current/lib/libnetcdf.a >> LIB_TCL = -ltcl8.4 >> LIB_TIFF = >> LIB_TIX = -ltix8.1.8.4 >> LIB_TK = -ltk8.4 >> LIB_UUID = /usr/lib64/libuuid.so >> LN_S = ln -s >> LTLIBOBJS = >> MAKEINFO = ${SHELL} /builddir/build/BUILD/freesurfer-6.0.0/config/missing >> makeinfo >> MKDIR_P = /usr/bin/mkdir -p >> MNI_CFLAGS = >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/1.5/include >> MNI_DIR = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/1.5 >> MNI_LIBS = >> -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/mni/1.5/lib >> MOC = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/bin/moc >> MPI_CFLAGS = >> MPI_DIR = >> MPI_LIB = >> MPI_LIBS = >> NIFTI_CFLAGS = >> NIFTI_DIR = >> NIFTI_LIB = >> NIFTI_LIBS = >> NVCC = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/CUDA/current/bin/nvcc >> NVCCFLAGS = -arch sm_11 --ptxas-options=-v -g >> OBJEXT = o >> OPENCL_CFLAGS = >> OPENCL_LIBS = >> OPENCV_CXXFLAGS = >> OPENCV_DIR = no >> OPENCV_LIBS = >> OPENMP_FLAG = -fopenmp >> OS = Linux >> OS_CPPFLAGS = >> OS_LDFLAGS = >> PACKAGE = freesurfer >> PACKAGE_BUGREPORT = >> freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> >> PACKAGE_NAME = Freesurfer >> PACKAGE_STRING = Freesurfer stable6 >> PACKAGE_TARNAME = freesurfer >> PACKAGE_URL = >> PACKAGE_VERSION = stable6 >> PATH_SEPARATOR = : >> PETSC_CFLAGS = >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/petsc/current/include >> PETSC_DIR = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/petsc/current >> PETSC_LIB = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/petsc/current/lib >> PETSC_LIBS = >> -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/petsc/current/lib >> POW_LIB = >> PTHREAD_CC = gcc >> PTHREAD_CFLAGS = >> PTHREAD_LIBS = >> QMAKE = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/bin/qmake >> QT_CFLAGS = -pipe -O2 -Wall -W -D_REENTRANT -fPIC $(QT_DEFINES) >> QT_CPPFLAGS = -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB >> -DQT_SCRIPT_LIB -DQT_SCRIPTTOOLS_LIB -DQT_CORE_LIB -I. -I. >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtOpenGL >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtWidgets >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtGui >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtScript >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtScriptTools >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtCore >> -I. >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/mkspecs/linux-g++ >> QT_CXXFLAGS = -pipe -O2 -std=gnu++0x -Wall -W -D_REENTRANT -fPIC >> $(QT_DEFINES) >> QT_DEFINES = -DQT_NO_DEBUG -DQT_OPENGL_LIB -DQT_WIDGETS_LIB -DQT_GUI_LIB >> -DQT_SCRIPT_LIB -DQT_SCRIPTTOOLS_LIB -DQT_CORE_LIB >> QT_DIR = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/bin/.. >> QT_INCPATH = -I. -I. >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtOpenGL >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtWidgets-I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtGui >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtScript >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtScriptTools >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/include/QtCore >> -I. >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/5.6.2/5.6/gcc_64/mkspecs/linux-g++ >> QT_LDFLAGS = -Wl,-O1 >> -Wl,-rpath,/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/lib >> >> -Wl,-rpath-link,/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/lib >> QT_LFLAGS = -Wl,-O1 >> -Wl,-rpath,/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/lib >> >> -Wl,-rpath-link,/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/lib >> QT_LIBS = >> -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/lib >> -lQt5OpenGL -L/usr/lib64 -lQt5Widgets -lQt5Gui -lQt5Script >> -L/usr/pubsw/packages/qt/5.6.2/5.6/gcc_64/lib -lQt5ScriptTools -lQt5Core >> -lGL -lpthread >> QT_PATH = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/bin >> QT_VERSION_MAJOR = 4 >> RANLIB = ranlib >> RCC = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/bin/rcc >> SET_MAKE = >> SHARED_CFLAGS = -fPIC >> SHARED_LDFLAGS = -shared >> SHELL = /bin/sh >> STRIP = strip >> TCL_CFLAGS = >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/tcltktixblt/current/include >> TCL_DIR = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/tcltktixblt/current >> TCL_LIB = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/tcltktixblt/current/lib >> TCL_LIBS = >> -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/tcltktixblt/current/lib >> TEEM_32BIT = 0 >> TEEM_DIO = 0 >> TEEM_ENDIAN = 1234 >> TEEM_QNANHIBIT = 1 >> TESTS_ENVIRONMENT = SURFER_FRONTDOOR=1 >> LD_LIBRARY_PATH=/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/tcltktixblt/current/lib:/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vtk/current/lib/vtk-5.6:/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/cppunit/current/lib >> TIFF_CFLAGS = >> TIFF_LIBS = >> TIXWISH = >> UIC = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/qt/current/bin/uic >> VERSION = stable6 >> VTK_CFLAGS = >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vtk/current/include/vtk-5.6 >> VTK_COCOA_CFLAGS = >> VTK_COCOA_CXXFLAGS = >> VTK_COCOA_DIR = >> VTK_COCOA_LIB = NO >> VTK_COCOA_LIBS = -LNO >> VTK_COCOA_LIB_VTK = >> VTK_CXXFLAGS = >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vtk/current/include/vtk-5.6 >> VTK_DIR = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vtk/current >> VTK_EXPAT_LIB = ../expat/libexpat.a >> VTK_FREETYPE_LIB = -lfreetype >> VTK_HDF5_LIB = >> VTK_JPEG_LIB = ../jpeg/libjpeg.a >> VTK_LIB = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vtk/current/lib/vtk-5.6 >> VTK_LIBS = >> -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vtk/current/lib/vtk-5.6 >> VTK_LIB_VTK = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vtk/current/lib/vtk-5.6 >> VTK_LSDYNA_LIB = >> VTK_METAIO_LIB = -lvtkmetaio >> VTK_MPEG2ENCODE_LIB = >> VTK_NETCDFCXX_LIB = >> VTK_PNG_LIB = -lvtkpng >> VTK_SQLITE_LIB = -lvtksqlite >> VTK_TIFF_LIB = ../tiff/libtiff.a >> VTK_VERDICT_LIB = -lvtkverdict >> VTK_Z_LIB = -lvtkzlib >> VXL_CFLAGS = >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vxl/current/include/vxl/core >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vxl/current/include/vxl/vcl >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vxl/current/include/vxl/v3p/netlib >> >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vxl/current/include/vxl/v3p/netlib/opt >> VXL_DIR = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vxl/current >> VXL_LIB = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vxl/current/lib >> VXL_LIBS = >> -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/vxl/current/lib >> WXWIDGETS_CFLAGS = >> -I/usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/wx/include/gtk2-ansi-release-static-2.8 >> -I/usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/include/wx-2.8 >> -D_FILE_OFFSET_BITS=64 -D_LARGE_FILES -D_LARGEFILE_SOURCE=1 -D__WXGTK__ >> -pthread >> WXWIDGETS_CXXFLAGS = >> -I/usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/wx/include/gtk2-ansi-release-static-2.8 >> -I/usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/include/wx-2.8 >> -D_FILE_OFFSET_BITS=64 -D_LARGE_FILES -D_LARGEFILE_SOURCE=1 -D__WXGTK__ >> -pthread >> WXWIDGETS_DIR = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/wxWidgets/current >> WXWIDGETS_GL_LIBS = -L/usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib -pthread >> -L/usr/X11R6/lib64 -L/usr/lib64 >> /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_gtk2_gl-2.8.a >> /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_base-2.8.a -lGL -lGLU >> -lz -ldl -lm >> WXWIDGETS_LIBS = -L/usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib -pthread >> -L/usr/X11R6/lib64 >> /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_gtk2_richtext-2.8.a >> /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_gtk2_aui-2.8.a >> /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_gtk2_xrc-2.8.a >> /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_gtk2_qa-2.8.a >> /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_gtk2_html-2.8.a >> /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_gtk2_adv-2.8.a >> /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_gtk2_core-2.8.a >> /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_base_xml-2.8.a >> /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_base_net-2.8.a >> /usr/pubsw/packages/wxWidgets/wxGTK-2.8.9/lib/libwx_base-2.8.a >> -Wl,--export-dynamic -pthread -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 >> -lgdk_pixbuf-2.0 -lpangoxft-1.0 -lpangox-1.0 -lpango-1.0 -lgobject-2.0 >> -lgmodule-2.0 -lgthread-2.0 -lglib-2.0 -lXinerama -lXxf86vm -lSM -lpng >> ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -lz -ldl -lm >> -lwx_gtk2_gl-2.8 >> WXWIDGETS_OPTIONAL_LIBS = >> XAWPLUS_CFLAGS = >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/xawplus/current/include >> XAWPLUS_CXXFLAGS = >> -I/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/xawplus/current/include >> XAWPLUS_DIR = >> /builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/xawplus/current >> XAWPLUS_LIBS = >> -L/builddir/build/BUILD/freesurfer-6.0.0/centos6-x86_64-packages/xawplus/current/lib >> XMKMF = >> XMLLINT = xmllint >> XXD = >> X_LIBS = -L/lib64 -lX11 -L/lib64 -lXmu >> abs_builddir = /builddir/build/BUILD/freesurfer-6.0.0/lta_convert >> abs_srcdir = /builddir/build/BUILD/freesurfer-6.0.0/lta_convert >> abs_top_builddir = /builddir/build/BUILD/freesurfer-6.0.0 >> abs_top_srcdir = /builddir/build/BUILD/freesurfer-6.0.0 >> ac_ct_CC = gcc >> ac_ct_CXX = g++ >> ac_ct_F77 = gfortran >> acx_pthread_config = >> am__include = include >> am__leading_dot = . >> am__quote = >> am__tar = tar --format=ustar -chf - "$$tardir" >> am__untar = tar -xf - >> bindir = /usr/bin >> build = x86_64-redhat-linux-gnu >> build_alias = x86_64-redhat-linux-gnu >> build_cpu = x86_64 >> build_os = linux-gnu >> build_vendor = centos4 >> builddir = . >> datadir = /usr/share >> datarootdir = ${prefix}/share >> docdir = ${datarootdir}/doc/${PACKAGE_TARNAME} >> dvidir = ${docdir} >> exec_prefix = /usr >> gl_cflags = >> gl_libs = >> host = Linux-centos4_x86_64 >> host_alias = x86_64-redhat-linux-gnu >> host_cpu = x86_64 >> host_os = linux-gnu >> host_vendor = centos4 >> htmldir = ${docdir} >> includedir = /usr/include >> infodir = /usr/share/info >> install_sh = ${SHELL} >> /builddir/build/BUILD/freesurfer-6.0.0/config/install-sh >> libdir = /usr/lib64 >> libexecdir = /usr/libexec >> localedir = ${datarootdir}/locale >> localstatedir = /var >> mandir = /usr/share/man >> mkdir_p = $(MKDIR_P) >> oldincludedir = /usr/include >> pdfdir = ${docdir} >> prefix = /opt/freesurfer/6.0.0 >> program_transform_name = s&^&& >> psdir = ${docdir} >> sbindir = /usr/sbin >> sharedstatedir = /var/lib >> srcdir = . >> sysconfdir = /etc >> target = x86_64-redhat-linux-gnu >> target_alias = >> target_cpu = x86_64 >> target_os = linux-gnu >> target_vendor = redhat >> top_build_prefix = ../ >> top_builddir = .. >> top_srcdir = .. >> AM_CFLAGS = -I$(top_srcdir)/include >> AM_CXXFLAGS = -I$(top_srcdir)/include >> BUILT_SOURCES = lta_convert.help.xml.h lta_convert.help.xml.html >> foodir = $(prefix)/docs/xml >> foo_DATA = lta_convert.help.xml >> foo2dir = $(prefix)/docs/html >> foo2_DATA = lta_convert.help.xml.html >> lta_convert_SOURCES = lta_convert.cpp >> lta_convert_LDADD = $(addprefix $(top_builddir)/, $(LIBS_MGH)) >> lta_convert_LDFLAGS = $(OS_LDFLAGS) >> >> # Our release target. Include files to be excluded here. 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for p in $${list[@]}; do \ >> echo "rm -fv $(prefix)/$(subdir)/$$p" >> >> $(prefix)/EXCLUDE_FILES_rm_cmds \;; \ >> done; \ >> list=( $(SUBDIRS) ); for subdir in $${list[@]}; do \ >> echo "Making release in $$subdir"; \ >> (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) release) \ >> || exit 1; \ >> done; >> >> # A rule for making the source tarball. It removes files declared in a >> # Makefile.am's EXCLUDE_FILES list (stuff that should not go outside the >> # NMR Center). >> dist-hook: >> list=( $(EXCLUDE_FILES) ); for p in $${list[@]}; do \ >> find $(distdir) -follow -name $$p -exec rm -Rf {} \;; \ >> done; \ >> extra_dist=( $(EXTRA_DIST) ); >> >> # A rule to create a header from an xml file in order to >> # include the file as a string at compilation time (see ProjectHelp wiki >> page) >> #%.xml.h : %.xml >> # xxd -i $< $@ >> >> # A rule to create an html file from an xml file (see ProjectHelp wiki page) >> %.xml.html : %.xml >> $(top_builddir)/utils/xmlToHtml $< $@ >> >> clean-local: >> rm -f $(BUILT_SOURCES) >> >> # Tell versions [3.59,3.63) of GNU make to not export all variables. >> # Otherwise a system limit (for SysV at least) may be exceeded. >> .NOEXPORT: >> >> * Oct 04, 2017, at 02:01:13 AM, Hoopes, Andrew >> <ahoo...@mgh.harvard.edu<mailto:ahoo...@mgh.harvard.edu>> wrote: >> If you cd into BUILD/freesurfer-6.0.0/lta_convert, does the file >> lta_convert.help.xml.h exist? >> Also, run ‘make' while in the lta_convert directory to see if the error >> output provides more details. If not, can you send me the contents of >> BUILD/freesurfer-6.0.0/lta_convert/Makefile? >> >> thanks >> Andrew >> >> On Oct 3, 2017, at 1:16 PM, Sol Jerome >> <s...@utdallas.edu<mailto:s...@utdallas.edu><mailto:s...@utdallas.edu>> >> wrote: >> >> I think so. I am actually attempting to build an RPM. Here is my spec >> file: >> >> >> Name: freesurfer >> Version: 6.0.0 >> Release: 1%{?dist} >> Summary: FreeSurfer Software Suite >> >> License: Proprietary >> URL: https://surfer.nmr.mgh.harvard.edu/ >> Source0: >> https://github.com/freesurfer/freesurfer#/%{name}-%{version}.tar.gz >> Source1: centos6-x86_64-packages.tar.gz >> >> BuildRequires: freetype-devel, gcc-gfortran, libtool, libuuid-devel, >> libXaw-devel, libXi-devel, mesa-libGLU-devel, netcdf-devel, tcsh >> BuildRequires: uuid-c++-devel, libXmu-devel, libpng-devel, lapack-static, >> blas-static >> #Requires: >> >> %description >> An open source software suite for processing and analyzing (human) >> brain MRI images. >> >> >> %prep >> %setup -q -a1 >> >> %build >> ./setup_configure >> %configure --disable-Werror --with-pkgs-dir=$(pwd)/centos6-x86_64-packages >> --prefix=/opt/%{name}/%{version} >> --with-mni-dir=$(pwd)/centos6-x86_64-packages/mni/1.5 >> >> %install >> make install DESTDIR=%{buildroot} >> >> %files >> %doc >> >> %changelog >> * Thu Sep 28 2017 Sol Jerome >> <s...@utdallas.edu<mailto:s...@utdallas.edu><mailto:s...@utdallas.edu>> - >> 6.0.0-1 >> - Initial freesurfer RPM >> >> >> >> >> >> >> Thanks, >> Sol >> >> * Oct 03, 2017, at 15:42:12 PM, Hoopes, Andrew >> <ahoo...@mgh.harvard.edu<mailto:ahoo...@mgh.harvard.edu><mailto:ahoo...@mgh.harvard.edu>> >> wrote: >> Hi Sol, >> >> I don't recognize this error, but will look into it. Have you set up the >> required system libraries and library dependencies described in >> https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page ? >> >> Andrew >> >> >> On Oct 2, 2017, at 5:55 PM, Sol Jerome >> <s...@utdallas.edu<mailto:s...@utdallas.edu><mailto:s...@utdallas.edu><mailto:s...@utdallas.edu>> >> wrote: >> >> Hi, >> >> I'm trying to build freesurfer on centos7 and I'm pretty sure that this >> failure is due to a missing build dependency. Can someone please help me >> determine what I'm missing? >> >> Making all in lta_convert >> make[2]: Entering directory >> `/builddir/build/BUILD/freesurfer-6.0.0/lta_convert' >> make[2]: Leaving directory >> `/builddir/build/BUILD/freesurfer-6.0.0/lta_convert' >> make[2]: *** No rule to make target `lta_convert.help.xml.h', needed by >> `all'. Stop. >> make[1]: *** [all-recursive] Error 1 >> make[1]: Leaving directory `/builddir/build/BUILD/freesurfer-6.0.0' >> make: *** [all] Error 2 >> >> >> >> Thanks, >> Sol >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
