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YNiC Analysis Tools
===================

This repository contains the YNiC analysis tools.
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Dependencies
============

Some of these aren't strict dependencies, but are instead what we develop
against (i.e. we don't guarantee not to use features which only exist from that
release onwards).  Package names are Debian binary package names.

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    python-numpy >= 1.11.0
    python-scipy >= 0.18.0
    python-matplotlib >= 1.5.3
    python-h5py >= 2.2.1
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    python-pil
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    python-dicom >= 0.9.8
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    python-nifti >= 0.20100607
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    python-sklearn >= 0.20
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    python-wxgtk3.0 >= 3.0.1
    python-yaml >= 3.11
    python-mpi4py >= 1.3.1
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    python-pyqt5 >= 5.3.2
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    python-pyqt5.qtopengl >= 5.3.2
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    pyqt5-dev-tools: >= 5.3.2
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    python-vtk >= 5.8
    python-bibtex >= 1.2.7
    libgsl0-dev >= 1.16
    fftw-dev >= 2.1.5
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    python-statsmodels >= 0.8
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    python-sphinx >= 1.2.3 (for building documentation and reports)
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    python-vtk >= 5.6
    python-bibtex >= 1.2.4
    libgsl0-dev >= 1.14
    fftw-dev >= 2.1.3
    python-sphinx >= 1.0.7
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    python-pytest and python.pytest-cov (for running the test suite)
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    xvfb (if building on a machine without an X display set)
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For use in MPI mode, you will also need:
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    openmpi-bin >= 1.6.5
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To co-register to standard space, you will need the MNI brain images installed.
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By default, NAF assumes that these are available in
/usr/share/fsl/data/standard Most programs will take the environment variables
NAFSTDBRAIN and NAFSTDMASK to override these paths if necessary.  If you want
to use freesurfer surfaces, you will require the fsaverage subject directory
(to match the MNI152 brain) which is set using NAFFSAVERAGEMRI:

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NAFSTDBRAIN defaults to /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz
NAFSTDMASK defaults to  /usr/share/fsl/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz
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NAFFSAVERAGEMRI defaults to /usr/share/freesurfer-5.1/subjects/fsaverage/mri/T1.mgz
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To use the nafMEGMakeCoreg script, you will need flirt, bet2 and betsurf from
the FSL suite.

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The following apt-get command should get all of the required dependencies:

apt-get install python-numpy python-scipy python-matplotlib python-h5py \
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                python-pil python-dicom python-nifti python-sklearn \
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                python-wxgtk3.0 python-yaml python-mpi4py python-pyqt5 \
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                python-pyqt5.qtopengl pyqt5-dev-tools python-vtk python-bibtex \
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                python-sphinx libgsl0-dev fftw-dev \
                python-statsmodels python-pytest python-pytest-cov
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You will also need build-essential and the relevant python development packages
installed.  A safe way to ensure you have it all is:

apt-get install build-essential python-all-dev

Mac OS X
========

We have not tried or tested the software under Mac OS X.  Bug reports are
welcome as long as they are accompanied by patches (or preferably git branches
to merge) as we don't have access to Mac boxes or the time to invest in fixing
the issues ourselves.

Windows Support
===============

There isn't any and is highly unlikely to be.