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 git@github.com:Danielhiversen/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
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