Hacks needed to build freesurfer - Freesurfer

8 Apr 2013


      I thought I'd share the changes I needed in order to build from the current
stable5 source in the repo.  I have a Raring Ubuntu distribution, and I
tried to install all the necessary libraries.  (Independent of building, I
still see https://bugzilla.redhat.com/show_bug.cgi?id=905638 in chklc.c of
stable5, but I've also commented that out in order to proceed.)
Needed updates (diffs below):
- Pulled missing unwarpGradientNonlinearity.{h,c} files from somewhere
   in Google's cache
   - Updates to configure.in:
   Bypass gcc 4.4 decision so that libtool is used correctly (Raring has
   uses 4.7)
   Correct the MNI libraries link order
   Change GL include directory
   Do not create glut Makfile/library (use glut from system)
   - Update several Makefile.am files to use glut from system
   - Configure options that I used:
   --disable-Werror
   --with-mni-dir=/usr
   --with-vxl-dir=/usr
   --with-tcl-include=/usr
   --with-gl-dir=/usr
   --x-libraries=/usr/lib/X11
   --x-includes=/usr/include/X11
? include/unwarpGradientNonlinearity.h
? utils/unwarpGradientNonlinearity.c
Index: configure.in
===================================================================
RCS file: /usr/fscvsroot/dev/configure.in,v
retrieving revision 1.519.2.39
diff -b -r1.519.2.39 configure.in
203,210c203,210
< ac_have_gcc_44="no"
< if test "${CC}" = "gcc"; then
<   gcc --version | head -n 1 | awk '{print $2 $3}' | grep "(GCC)4.4." >&
/dev/null
<   if test "$?" = "0"; then
<     AC_MSG_NOTICE(Have gcc 4.4)
<     ac_have_gcc_44="yes"
<   fi
< fi
---
...
ac_have_gcc_44="yes"
# if test "${CC}" = "gcc"; then
#   gcc --version | head -n 1 | awk '{print $2 $3}' | grep "(GCC)4.4." >&
/dev/null
...
#   if test "$?" = "0"; then
#     AC_MSG_NOTICE(Have gcc 4.4)
#     ac_have_gcc_44="yes"
#   fi
#fi
1229c1229
<   LIBS_MNI="-lnetcdf -lhdf5 -lvolume_io2 -lminc2"
---
...
LIBS_MNI="-lvolume_io2 -lminc2 -lnetcdf -lhdf5"
2748c2748
<   [  ac_gl_includes="$withval"/include
---
...
[  ac_gl_includes="$withval"/include/GL
3472d3471
<            glut/Makefile
Index: fsgdf/fsgdf_wrap.c
===================================================================
RCS file: /usr/fscvsroot/dev/fsgdf/fsgdf_wrap.c,v
retrieving revision 1.18
diff -b -r1.18 fsgdf_wrap.c
110c110
< #include <tcl.h>
---
...
#include <tcl8.5/tcl.h>
Index: Makefile.am
===================================================================
RCS file: /usr/fscvsroot/dev/Makefile.am,v
retrieving revision 1.224.2.13
diff -b -r1.224.2.13 Makefile.am
13d12
< glut \
Index: mri_probedicom/Makefile.am
===================================================================
RCS file: /usr/fscvsroot/dev/mri_probedicom/Makefile.am,v
retrieving revision 1.7
diff -b -r1.7 Makefile.am
5c5
< AM_CFLAGS=-I$(top_srcdir)/glut $(GL_CFLAGS) \
---
...
AM_CFLAGS=$(GL_CFLAGS) \
14c14
< $(X_LIBS) $(LIBS_OPENGL) $(top_builddir)/glut/libglut.a
---
...
$(X_LIBS) $(LIBS_OPENGL) -lglut
Index: mris2rgb/Makefile.am
===================================================================
RCS file: /usr/fscvsroot/dev/mris2rgb/Makefile.am,v
retrieving revision 1.8
diff -b -r1.8 Makefile.am
14d13
< -I$(top_srcdir)/glut \
26,27c25
< $(LIBS_OPENGL) -lGL $(LIBTIFF) \
< $(top_builddir)/glut/libglut.a
---
...
$(LIBS_OPENGL) -lGL -lX11 $(LIBTIFF) -lglut
Index: mris_show/Makefile.am
===================================================================
RCS file: /usr/fscvsroot/dev/mris_show/Makefile.am,v
retrieving revision 1.7
diff -b -r1.7 Makefile.am
6d5
< -I$(top_srcdir)/glut \
15c14
< $(LIBS_OPENGL) $(top_builddir)/glut/libglut.a
---
...
$(LIBS_OPENGL) -lglut
Index: nmovie/Makefile.am
===================================================================
RCS file: /usr/fscvsroot/dev/nmovie/Makefile.am,v
retrieving revision 1.11.4.3
diff -b -r1.11.4.3 Makefile.am
10,11c10
< -I$(top_srcdir)/unix \
< -I$(top_srcdir)/glut
---
...
-I$(top_srcdir)/unix
16,17c15
< -I$(top_srcdir)/unix \
< -I$(top_srcdir)/glut
---
...
-I$(top_srcdir)/unix
27c25
< $(top_builddir)/glut/libglut.a
---
...
-lglut
31c29
< $(top_builddir)/glut/libglut.a
---
...
-lglut
Index: stim_polar/Makefile.am
===================================================================
RCS file: /usr/fscvsroot/dev/stim_polar/Makefile.am,v
retrieving revision 1.9
diff -b -r1.9 Makefile.am
7c7
< -I$(top_srcdir)/glut $(GL_CFLAGS)
---
...
$(GL_CFLAGS)
14c14
< $(X_LIBS) $(LIBS_OPENGL) $(top_builddir)/glut/libglut.a
---
...
$(X_LIBS) $(LIBS_OPENGL) -lglut