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README.md

Phantomas

Phantomas (http://www.emmanuelcaruyer.com/phantomas.php) is an open-source software library for the creation of realistic phantoms in diffusion MRI. This is intented as a tool for the validation of methods in acquisition, signal and image processing, local reconstruction and fiber tracking in diffusion MRI. Phantomas is released under the terms of the revised BSD license. You should have received a copy of the license together with the software, please refer to the file ''LICENSE''.

Dependencies

Phantomas is written in Python with parts in C. You will need Python 2.7, and Cython installed on your computer.

Besides, Phantomas depends on:

  • numpy,
  • scipy,
  • scikits-sparse

Optionally, you may also need:

  • vtk,
  • matplotlib.

Dependencies can be satisfied by running pip install -r requirements.txt

On ubuntu 14.04, installation of scikits-sparse by pip (pip install scikits.sparse) failed with the following line: scikits/sparse/cholmod.c:245:33: fatal error: suitesparse/cholmod.h: No such file or directory The issue was solved installing the package 'libsuitesparse-dev': apt-get install libsuitesparse-dev

Build instructions

Under linux, simply run (as root)

python setup.py install

Getting started

Phantomas provides a number of scripts, and examples. The main script is phantomas_dwis. For more info, type:

$ phantomas_dwis -h

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Create realistic digital phantoms in diffusion MRI.

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