Local Install¶
Steps to setup/run MIRACL on a Linux / Mac OS X machine:
git clone https://github.com/mgoubran/MIRACL.git miracl
(or download the zip file containg the repo and uncompress it), then:
cd miracl
To setup a virtual environment, download Anaconda for Python 2.7: https://www.anaconda.com/distribution/#download-section,
Then create the environment:
conda create --name miracl python=3.7.4 pip
conda activate miracl
install Dependencies
pip install -e .
ANTS & c3d¶
Place the depends folder inside linux_depends or mac_depends (based on your OS), found here:
inside the miracl folder
mv ~/Downloads/depends.zip miracl/.
cd miracl
unzip depends.zip
rm depends.zip
This folder contains compiled versions of ANTS and c3d for Linux or Mac OS. Before continuing, make sure to change the permissions. This can be done by running
chmod -R 755 {path/to/depends}/*
In order to run the pipeline, some symbolic links must be added to access certain commands. Inside the miracl folder, run:
sudo ln -s {path/to/depends}/ants/antsRegistrationMIRACL.sh /usr/bin/ants_miracl_clar && chmod +x /usr/bin/ants_miracl_clar
sudo ln -s {path/to/depends}/ants/antsRegistrationMIRACL_MRI.sh /usr/bin/ants_miracl_mr && chmod +x /usr/bin/ants_miracl_mr
Make sure {path/to/depends} is replaced with the directory path that leads to the depends directory .
Allen atlases¶
Place the atlases folder in the same link above inside the miracl folder
mv ~/Downloads/atlases.zip miracl/.
cd miracl
unzip atlases.zip
rm atlases.zip
This folder contains the Allen atlas data needed for registration and connectivity analysis
Fiji & FSL¶
install Fiji & FSL:
for Linux:
cd depends
wget https://downloads.imagej.net/fiji/latest/fiji-linux64.zip
unzip fiji-linux64.zip
rm fiji-linux64.zip
install additional plugins by:
going to Help -> Update and press “Manage update sites” button and
choose the following update sites there:
3D ImageJ Suite: http://sites.imagej.net/Tboudier
Biomedgroup: https://sites.imagej.net/Biomedgroup
IJPB-plugins: http://sites.imagej.net/IJPB-plugins
wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py
sudo python fslinstaller.py
Visualization¶
For the visualization of nifti files and labels we recommend ITKSNAP
or the nifti plugin for Fiji/ImageJ
Diffusion Data¶
If you have diffusion MRI data install:
sudo apt-get install git g++ python python-numpy libeigen3-dev zlib1g-dev libqt4-opengl-dev libgl1-mesa-dev libfftw3-dev libtiff5-dev
git clone https://github.com/MRtrix3/mrtrix3.git
cd mrtrix3
./configure
./build
./set_path
Troubleshooting¶
Please refer to our Troubleshooting section.