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volgenmodel-nipype

Port of volgenmodel to Nipype. Interfaces to MINC tools that were previously in this repo are now in the master branch of Nipype.

Install

Prerequisites

minc-toolkit / minc-widgets

On Debian/Ubuntu systems:

sudo apt-get install octave cmake cmake-curses-gui \
                     build-essential g++ \
                     cmake cmake-curses-gui \
                     bison flex \
                     freeglut3 freeglut3-dev \
                     libxi6 libxi-dev libxmu6 libxmu-dev libxmu-headers

Build minc-toolkit from Github:

git clone --recursive git://github.com/BIC-MNI/minc-toolkit.git minc-toolkit
cd minc-toolkit
rm -fr build
mkdir build
cd build
cmake -DMT_BUILD_SHARED_LIBS=ON -DMT_BUILD_VISUAL_TOOLS=ON ..
make &> make.log   # check the log!
sudo make install  # installs to /usr/local

You should also end up with the tools from https://github.com/BIC-MNI/minc-widgets

nipype

Install the latest from Github:

sudo apt-get install python-nibabel python-traits python-future python-simplejson
sudo pip install prov

git clone https://github.com/nipy/nipype
cd nipype
sudo python setup.py install

bestlinreg and minccomplete

The scripts bestlinreg and minccomplete are included in this repository in extra-scripts.

Running

Then:

git clone https://github.com/carlohamalainen/volgenmodel-nipype
cd volgenmodel-nipype
export PYTHONPATH=`pwd`
export PATH=$PATH:`pwd`/extra-scripts
export PERL5LIB=/usr/local/perl  # assuming minc-toolkit is installed in /usr/local

Load the volgenmodel.py script using IPython or similar, being sure to tweak FAST_EXAMPLE_BASE_DIR to something appropriate. Then

workflow.run()

runs the workflow on a single core, or

workflow.run(plugin='MultiProc', plugin_args={'n_procs' : 4})

runs it on 4 cores.

The workflow for a small 3-stage model is:

workflow fast-example

The final output is in $FAST_EXAMPLE_BASE_DIR/volgenmodel_final_output.

Vagrant/Puppet

(Old, probably doesn't work now.)

Vagrant/Puppet scripts are here: vagrant-puppet.

Docker

See volgenmodel-nipype/docker for a script to run a sample mouse brain workflow. This uses a sample mouse brain model which is available in a separate repository (around 96Mb in size): https://github.com/carlohamalainen/volgenmodel-fast-example.git

The final model should look like this:

mouse model triplanar

Citation

This method is an implementation of the technique described in this paper:

http://www.ncbi.nlm.nih.gov/pubmed/25620005

If you use it in a publication please cite:

Janke AL, Ullmann JF, Robust methods to create ex vivo minimum deformation atlases for brain mapping. Methods. 2015 Feb;73:18-26. doi: 10.1016/j.ymeth.2015.01.005.