volgenmodel-nipype

This is the original development repo from 2014.

Official repository: https://github.com/NIF-au/volgenmodel-nipype

Active fork at CAI-UQ: https://github.com/CAIsr/volgenmodel-nipype

volgenmodel-nipype is the port of volgenmodel to Nipype. It creates nonlinear models from a series of input MINC files.

Quickstart on Ubuntu 20 with MINC Toolkit 1.9.18-20200813

Ubuntu packages

sudo apt-get install git octave python3-pip imagemagick

minc-toolkit

From https://bic-mni.github.io/#installing:

wget http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.18-20200813-Ubuntu_20.04-x86_64.deb
sudo dpkg -i minc-toolkit-1.9.18-20200813-Ubuntu_20.04-x86_64.deb

nipype

pip install nipype

Run the fast example

git clone https://github.com/carlohamalainen/volgenmodel-nipype
git clone https://github.com/carlohamalainen/volgenmodel-fast-example.git

cd volgenmodel-nipype
export PYTHONPATH=`pwd`
export PATH=$PATH:`pwd`/extra-scripts:/opt/minc/1.9.18/bin
export PERL5LIB=/opt/minc/1.9.18/perl

python3 volgenmodel.py --run=MultiProc --ncpus=2 --fit_stages=lin,1,3 --input_dir=../volgenmodel-fast-example

Check the output:

$ find workflow_output_workflowMultiProc2/ -type f
workflow_output_workflowMultiProc2/stdev/mouse00_volcentre_norm_resample_bigaverage_stdev_vol_symm.mnc
workflow_output_workflowMultiProc2/model/mouse00_volcentre_norm_resample_bigaverage_reshape_vol_symm.mnc

Install for Windows Subsystem for Linux or Ubuntu 16.04

Install minc: https://bic-mni.github.io

    wget http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.16-20180117-Ubuntu_16.04-x86_64.deb
    sudo apt-get install libc6 libstdc++6 imagemagick perl octave
    sudo dpkg -i minc-toolkit-1.9.16-20180117-Ubuntu_16.04-x86_64.deb
    sudo apt-get install libgl1-mesa-glx libglu1-mesa
    rm minc-toolkit-1.9.16-20180117-Ubuntu_16.04-x86_64.deb

    vi .bashrc
    source /opt/minc/1.9.16/minc-toolkit-config.sh
    export PERL5LIB=/opt/minc/1.9.16/perl

Clone code and test-data:

git clone https://github.com/CAIsr/volgenmodel-nipype.git
git clone https://github.com/CAIsr/volgenmodel-fast-example.git

install miniconda:

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

start new terminal and install packages required:

conda install --channel conda-forge nipype
pip install pydot

add additonal scripts to PATH

cd volgenmodel-nipype/extra-scripts
echo "export PATH="`pwd -P`":\$PATH" >> ~/.bashrc

you need a working octave installed. Somehow the minc libs break octave. Sometimes this fixes it: select /usr/lib/lapack/liblapack.so.3

sudo update-alternatives --config liblapack.so.3

or load octave using a module:

module load octave/4.2.1

start new temrinal and run volgenmodel with the test data:

cd volgenmodel-nipype/
python3 volgenmodel.py --input_dir ../volgenmodel-fast-example

The final model should look like this:

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