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:

download link

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:

Fiji/ImageJ

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

FSL

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:

MRtrix3

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

Deactivate

To end session

conda deactivate

Update MIRACL

To update MIRACL, run

cd miracl
git pull

You should be good to go!

Troubleshooting

Q: I get the following error whenever I try to run the GUI: qt.qpa.plugin: Could not load the Qt platform plugin “xcb” in “{anaconda path}/envs/miracl_merge/lib/python3.7/site-packages/cv2/qt/plugins” even though it was found.

If you know the path to the environment name, try running the following line to remove the specific file in question:

rm "{path_to_environment_name}/lib/python3.7/site-packages/cv2/qt/plugins/platforms/libqxcb.so"