Merge branch 'dev' of github.com:freesurfer/freesurfer into rf-ident

GEMS2/CMakeLists.txt

@@ -33,6 +33,8 @@ OPTION( BUILD_GUI "Build GUI components (requires FLTK and VTK)" OFF )
 
 OPTION( BUILD_MATLAB "Build Matlab wrappers" OFF )
 
+OPTION( BUILD_CUDA "Build CUDA stuff" OFF )
+
 #
 IF( BUILD_EXECUTABLES OR BUILD_GUI )
   #
@@ -45,20 +47,19 @@ IF( BUILD_EXECUTABLES OR BUILD_GUI )
 ENDIF( BUILD_EXECUTABLES OR BUILD_GUI )
 
 
+IF( BUILD_CUDA )
+  FIND_PACKAGE( CUDA )
+  IF( CUDA_FOUND )
+    # Enable C++11 syntax
+    SET(CMAKE_CXX_FLAGS "-g -std=c++11 ${CMAKE_CXX_FLAGS}")
 
+    INCLUDE_DIRECTORIES(${CUDA_INCLUDE_DIRS})
+    SET(CMAKE_CXX_FLAGS "-DCUDA_FOUND ${CMAKE_CXX_FLAGS}")
 
-# Find CUDA
-FIND_PACKAGE( CUDA )
-IF( CUDA_FOUND )
-  # Enable C++11 syntax
-  SET(CMAKE_CXX_FLAGS "-g -std=c++11 ${CMAKE_CXX_FLAGS}")
-
-  INCLUDE_DIRECTORIES(${CUDA_INCLUDE_DIRS})
-  SET(CMAKE_CXX_FLAGS "-DCUDA_FOUND ${CMAKE_CXX_FLAGS}")
-
-  INCLUDE_DIRECTORIES(cuda)
-  SUBDIRS(cuda)
-ENDIF( CUDA_FOUND )
+    INCLUDE_DIRECTORIES(cuda)
+    SUBDIRS(cuda)
+  ENDIF( CUDA_FOUND )
+ENDIF( BUILD_CUDA )
 
 
 # Add libary

GEMS2/fs_build_GEMS2

@@ -0,0 +1,34 @@
+#! /bin/bash -ef
+set -eu
+
+export CC="`which cc`"
+export CXX="`which c++`"
+export AR="`which ar`"
+export RANLIB="`which ranlib`"
+
+rm -Rf CMakeCache.txt CMakeFiles/ CMakeTmp/
+
+cmake . -G "Unix Makefiles" \
+-DBUILD_CUDA=OFF \
+-DBUILD_EXECUTABLES=OFF \
+-DBUILD_GUI=OFF \
+-DBUILD_MATLAB=OFF \
+-DBUILD_SHARED_LIBS=OFF \
+-DBUILD_TESTING=OFF \
+-DITK_DIR=../itk-5.0/build \
+-DCMAKE_BUILD_TYPE=Release \
+-DCMAKE_CXX_COMPILER=$CXX \
+-DCMAKE_CXX_COMPILER_AR=$AR \
+-DCMAKE_CXX_COMPILER_RANLIB=$RANLIB \
+-DCMAKE_CXX_FLAGS="-msse2 -mfpmath=sse -fPIC -fpermissive" \
+-DCMAKE_C_COMPILER=$CC \
+-DCMAKE_C_COMPILER_AR=$AR \
+-DCMAKE_C_COMPILER_RANLIB=$RANLIB \
+-DCMAKE_C_FLAGS="-msse2 -mfpmath=sse -fPIC -fpermissive" \
+-DCMAKE_VERBOSE_MAKEFILE=ON \
+-DCMAKE_INSTALL_PREFIX=.
+
+make clean
+make -j 8
+#make test
+#make install

Makefile.smalldist.am

@@ -1,15 +1,19 @@
 ##
 ## Makefile.smalldist.am
 ##
-## This makes only the binaries needed to run recon-all -all -no-ba-labels, ie. a minimal install.
-## To use: 
-## cp Makefile.smalldist.am Makefile.am
-## include --enable-small-dist-install with configure to reduce data files installed
-## include --disable-g with configure to compile without debug symbols
-## include --disable-GUI-build with configure to disable build of GUI apps (eg. freeview)
-## then run the usual: setup_configure, configure, make, make install, make install-data-hook
+## This makes only the binaries needed to run recon-all -all , ie. a minimal install.
+## To use, just include the flag --enable-small-build-dist with configure.  That will
+## disable the build of the GUI apps, and enable the 'small dist' data install, and
+## replace Makefile with this Makefile.smalldist.  One could also include --disable-g 
+## with configure to compile without debug symbols.
+## For a working installation, the MNI tools (namely nu_correct) will need to be 
+## installed, so one with need to include --with-mni-dir=somepathtomnidir so that
+## during make install, the link is made in freesurfer/mni to those tools.
 ##
 
+## TODO: this list could use some trimming based on a reprozip analysis to figure-out
+## the true list of source files needed
+
 ACLOCAL_AMFLAGS=-I m4
 
 foodir=$(prefix)
@@ -18,6 +22,7 @@ foo_DATA=LICENSE NOTICE README AUTHORS INSTALL COPYING
 MRISUBDIRS=\
 	lta_convert \
 	mri_jacobian \
+	mri_and \
 	mri_add_xform_to_header \
 	mri_annotation2label \
 	mri_aparc2aseg \
@@ -29,22 +34,36 @@ MRISUBDIRS=\
 	mri_cc \
 	mri_compute_overlap \
 	mri_concat \
+	mri_compute_seg_overlap \
+	mri_concatenate_lta \
 	mri_convert \
+	mri_coreg \
 	mri_deface \
 	mri_diff \
 	mri_edit_segmentation \
 	mri_edit_segmentation_with_surfaces \
+	mri_edit_wm_with_aseg \
+	mri_extract_largest_CC \
 	mri_em_register \
+	mri_fuse_segmentations \
+	mri_gcut \
 	mri_fill \
 	mri_fwhm \
 	mri_info \
-	mri_and \
 	mri_label2label \
 	mri_label2vol \
+	mri_log_likelihood \
+	mri_normalize \
+	mri_normalize_tp2 \
+	mri_mask \
+	mri_mc \
+	mri_matrix_multiply \
 	mri_relabel_hypointensities \
 	mri_relabel_nonwm_hypos \
 	mri_remove_neck \
 	mri_robust_register \
+	mri_segment \
+	mri_segreg
 	mri_surf2surf \
 	mri_surf2vol \
 	mri_surfcluster \
@@ -55,18 +74,12 @@ MRISUBDIRS=\
 	mri_stats2seg \
 	mri_vol2surf \
 	mri_watershed \
-	mri_edit_wm_with_aseg \
-	mri_extract_largest_CC \
-	mri_compute_seg_overlap \
-	mri_concatenate_lta \
-	mri_log_likelihood \
 	talairach_afd \
 	talairach_avi
 
 MRISSUBDIRS=\
 	mris_calc \
 	mris_anatomical_stats \
-	mris_transmantle_dysplasia_paths \
 	mris_average_curvature \
 	mris_ca_label \
 	mris_divide_parcellation \
@@ -85,6 +98,7 @@ MRISSUBDIRS=\
 	mris_diff \
 	mris_register \
 	mris_left_right_register \
+	mrisp_paint \
 	mris_smooth \
 	mris_sphere \
 	mris_thickness \
@@ -110,7 +124,9 @@ COREDIRS=\
 	scripts \
 	distribution \
 	fsgdf \
-	hipsstubs
+	hipsstubs \
+	tetgen \
+	tkregister2
 
 # dependent on COREDIRS
 OTHERDIRS=\
@@ -169,6 +185,9 @@ EXTRA_DIST=setup_configure Makefile.extra x86cpucaps \
 
 DISTCLEANFILES=cpuflags.mak
 
+distclean-hook:
+	rm -f Makefile
+
 # we have files in our dist that dont and shouldnt get cleaned, like testdata.
 # this target override allows make distcheck to pass
 distcleancheck: