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updated ANTs compile instructions: ITKv4

latest ants binaries are here:   ANTs-Binaries

instructions for linux / osx type installation.   windows works too ( via cmake ) but i dont have specifics.

to compile ants from the source code, you first need: git, cmake and a c++ compiler

then in a terminal, do:

>  git clone git://github.com/stnava/ANTs.git

>  mkdir antsbin

> cd antsbin

>  ccmake ../ANTs

then go into cmake and type “c” and then “g”  then exit back to the
terminal.   then:

>  make -j 4

and wait a while.

to update an existing ANTs install, go to the ANTs directory and type “git pull origin master”

Don’t forget to toggle to advanced and turn off

SuperBuild_ANTS_USE_GIT_PROTOC if behind firewall


gcc 4.6.1 on osx lion

got gcc 4.6.1 installed on lion.   why do you want gcc?

basically, better warnings, faster compilation and better optimization.   i was mainly interested in the fact that it finds errors that lion’s 4.2 misses.

i tried to simplify these instructions a bit (which are excellent):

http://solarianprogrammer.com/2011/09/20/compiling-gcc-4-6-1-on-mac-osx-lion/

if you have homebrew installed, the first couple steps become:

1.  brew install gmp

2.  brew install mpfr
3.  then get mpc 0.8.1 from here:
../configure --prefix=$HOME/my_gcc --with-gmp=/usr/local/Cellar/gmp/5.0.2/lib/ --with-mpfr=/usr/local/Cellar/mpfr/3.0.1/lib/
 make
 make install
note — you may get an error similar to this:
in that case open the relevant failing file and replace GMP_RND with MPFR_RND
then compile gcc 4.6 via :
../configure --prefix=$HOME/my_gcc --enable-checking=release --with-gmp=/usr/local/Cellar/gmp --with-mpfr=/usr/local/Cellar/mpfr --with-mpc=/Users/stnava/my_gcc/ --program-suffix=-4.6.1
make   # could take all day
sudo make install
then create a Makefile:
CFLAGS=-c -Wall
LDFLAGS=
SOURCES=test.cpp
OBJECTS=$(SOURCES:.cpp=.o)
EXECUTABLE=hello
all: $(SOURCES) $(EXECUTABLE)
$(EXECUTABLE): $(OBJECTS)
    $(CC) $(LDFLAGS) $(OBJECTS) -lpthread -std=c++0x  -o $@
.cpp.o:
    $(CC) $(CFLAGS) $< -o $@
in the Makefile, the $(CC) lines shoudl begin with a tab, all others left-justified.
then compile the test.cpp by typing make.
#include <iostream>
using namespace std;
int main()
{
// below some funky new C++0x syntax ( the next ISO C++ standard. )
  cout<<[](int m,int n){return m+n;}(2,4)<<endl;
  std::cout <<" go surfing " << std::endl;
  return(0);
}
it should print the number 6 then say "go surfing."


surface analysis and normalization environment


Reliable neuroimage processing: a pipedream?

Pipedream (@ sourceforge) in action on the Oasis dataset.   DiReCT for cortical thickness measurement.  Atropos for segmentation.

DiReCT – Diffeomorphic registration based cortical thickness (DiReCT)


Glamorous Glue

the paper


Brain Code Set