ITK: Compile ITK with minc2 support

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Revision as of 19:04, 11 June 2024 by Jblocher (talk | contribs) (Created page with "== 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...")
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Build netCDF 3.6.3

NetCDF[1] (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[2]

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[3] 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[4] (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)[5]. 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
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