Step by step installation of dependencies on Ubuntu - SyneRBI/SIRF GitHub Wiki

This page documents step-by-step installation of dependencies on Ubuntu. It is probably better to follow the instructions that use our installation scripts. The list of dependencies here might be out-of-date for instance.

SIRF dependencies

 sudo apt install build-essential git g++

You probably want Python support

sudo apt install python3-dev python3-pip python3-tk 
python3 -m pip install --upgrade pip wheel setuptools
python3 -m pip install --only-binary=numpy,scipy,matplotlib numpy matplotlib nose coverage docopt

One of the PET Python demos (steepest_ascent.py) requires scipy.

python3 -m pip install scipy

Please check also our pages with specific instructions for SIRF and MATLAB, and SIRF and Python.

Gadgetron dependencies

 sudo apt install \
    h5utils \ 
    liblapack-dev \
    libace-dev 

With the SIRF SuperBuild also the siemens_to_ismrmrd package can be installed. This package allows for the transformation of Siemens MR raw data to the ISMRMRD raw data format, which is the format used by SIRF for MR raw and image data. Siemens_to_ismrmrd requires the following dependencies:

    libxml2-dev \     
    libxslt-dev 

Installing the following will add extra functionality to Gadgetron which you might want (but are currently not used by SIRF).

    python3-h5py \
    python3-libxml2 \
    python3-psutil \
    libplplot-dev 

Optionally install CUDA suport if you have a NVidia GPU

  sudo apt install nvidia-cuda-toolkit 

Optionally install MKL, see our separate page including some info on harmless warnings you will get if you don't install MKL.