NeuroImageRegistration

Install

http://neuro.debian.net/install_pkg.html?p=fsl-complete

sudo apt-get install -y libblas-dev liblapack-dev libfreetype6-dev
sudo apt-get install -y cmake ninja-build git
sudo apt-get install gfortran

git clone git://github.com/stnava/ANTs.git
mkdir antsbin
cd antsbin
cmake -G "Ninja" -DCMAKE_BUILD_TYPE=Release ../ANTs/
ninja

sudo apt-get install python-pip
cd
git clone https://github.com/SINTEFMedtek/NeuroImageRegistration.git
cd NeuroImageRegistration/
virtualenv venv
source venv/bin/activate
sudo pip install --upgrade setuptools
sudo pip install --upgrade distribute
pip install -r requirements.txt

ant registration parameters inspired by http://miykael.github.io/nipype-beginner-s-guide/normalize.html https://apps.icts.uiowa.edu/confluence/display/BRAINSPUBLIC/ANTS+conversion+to+antsRegistration+for+same+data+set

Usage

Some computer specific pathes must be sat in util.py

• ConvertDataToDB.py,
• ConvertDataToDB_menigiomer.py and
• ConvertDataToDB_MM.py

are used to convert the data and add it to a database

• do_img_registration.py,
• do_img_registration_GBM.py,
• do_img_registration_LGG_POST.py,
• do_img_registration_LGG_PRE.py and
• do_img_registration_MM.py

are used do registration of the volume to a reference volume.

• run_neuro_reg.sh,
• run_neuro_reg_gbm.sh,
• run_neuro_reg_gbm2.sh,
• run_neuro_reg_gbm3.sh and
• run_neuro_reg_gbm_post.sh

are used to do the image registration on a super computer

• postProcess.py,
• postProcess_GBM.py and
• postProcess_MM.py

are used post processing and generating figures