ndreg-old

NeuroData's registration library, built in python using ITK

Submit bug reports here.

Installation

Easy way

The easiest way to install ndreg with docker. To build a new Docker image: docker build . -t ndreg-jupyter

To run and test with a sample notebook on port 8888: docker run -p 8888:8888 ndreg-jupyter

If you want to save notebooks, you will need to mount a local path, e.g: docker run -p 8888:8888 -v pwd/notebooks:/run/notebooks ndreg-jupyter

Hard way

More advanced users can build ndreg from scratch

Installating dependances on Ubuntu 16.04 and later

• Install dependancies

sudo apt-get -y install cmake python-numpy libinsighttoolkit4-dev libfftw3-dev

• Proceded to Installing ndreg

Installing dependances other linux distributions

• Build and install ITK 4.10.0 or later

  itkVersion=4.10.0
  itkMinorVersion=`echo ${itkVersion} | cut -d'.' -f 1,2`
  mkdir itk; cd itk
  wget https://sourceforge.net/projects/itk/files/itk/${itkMinorVersion}/InsightToolkit-${itkVersion}.tar.gz
  tar -vxzf InsightToolkit-${itkVersion}.tar.gz
  mv InsightToolkit-${itkVersion} src/
  mkdir bin; cd bin
  cmake -G "Unix Makefiles" -DITK_USE_SYSTEM_FFTW=OFF -DITK_USE_FFTWD=ON -DITK_USE_FFTWF=ON -DModule_ITKReview=ON ../src 
  make && sudo make install

• For Ubuntu 15.10 and earlier

  • Install dependances

  sudo apt-get -y install cmake

  • Proceded to Installing ndreg

• For Centos 6.7 and later

  • Install dependances

    sudo yum -y install libjpeg-devel cmake 
    sudo /usr/local/bin/pip install  --trusted-host www.simpleitk.org -f http://www.simpleitk.org/SimpleITK/resources/software.html SimpleITK
    sudo /usr/local/bin/pip install blosc==1.3.0

  • Proceded to Installing ndreg

Installing ndreg

git clone https://github.com/neurodata/ndreg.git
cd ndreg
cmake .
make && sudo make install