View source for ITK: Compile ITK with minc2 support

== Build netCDF 3.6.3 ==
NetCDF[http://www.unidata.ucar.edu/software/netcdf/] (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

The newest version is 4.0.1, but it seems that minc2 does not compiles with this version. Use 3.6.3.
 
    ./configure --prefix=/usr/local --enable-shared
     make
     make install

== Build HDF5 1.6.9 ==

HDF5 needs zlib and szip libraries. Both of them need to be built before configuring HDF5. you can get zlib and szip form HDF5 web page[http://www.hdfgroup.org/HDF5/release/obtain516.html]
==== build szip 2.1  ====
    cd szip-2.1
    ./configure --prefix=/usr/local --enable-shared
    make
    make install
==== build zlib 1.2.3 ====
    cd zlib-1.2.3
    ./configure --prefix=/usr/local --shared
    make
    make install

HDF5[http://www.hdfgroup.org/HDF5/] is a unique technology suite that makes possible the management of extremely large and complex data collections.

Current Release versions include HDF5 1.8.3 & HDF5 1.6.9. Use HDF5 1.6.9 for MINC2.

    ./configure --prefix=/usr/local --enable-shared --with-zlib=/usr/local --with-szlib=/usr/local
    make
    make install

== Build MINC2 2.0.18 ==
MINC[http://www.nitrc.org/softwaremap/trove_list.php?form_cat=475] (Medical Image NetCDF ) is primarily a file format and a 3 level API for medical image analysis with a particular focus on the needs of research. MINC is a software system for storing and manipulating medical images, originally developed in 1993 by Peter Neelin at the McConnell Brain Imaging Centre.

    ./configure --prefix=/usr/local --enable-shared
    make
    make install

== Build ITK 3.16.0  with MINC2 2.0.18 support ==
Insight Segmentation and Registration Toolkit (ITK)[http://itk.org/].  ITK is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis.  Developed through extreme programming methodologies, ITK employs leading-edge algorithms for registering and segmenting multidimensional data. 

Set the variables as follows in cmake, then make and make install. 

    HDF5_INCLUDE_PATH     /usr/local/include  
    HDF5_LIB              /usr/local/lib/libhdf5.so
    MINC2_INCLUDE_PATH    /usr/local/include                                   
    MINC2_LIB             /usr/local/lib/libminc2.so                           
    MINC_INCLUDE_PATH     /usr/local/include                                   
    NETCDF_INCLUDE_PATH   /usr/local/include                                   
    NETCDF_LIB            /usr/local/lib/libnetcdf.so 
    ITK_USE_MINC2         ON
    ITK_USE_REVIEW        ON