mia_processes

Documentation

The documentation is available in mia_processes's website.

Installation

• A compatible version of Python (>= 3.5) and pip must be installed.

• Depending on the Python setup and OS, the python3 command may be used as the default Python command.

  Try: python -V

  If it returns Python 3.x.x, replace all the python3 commands below by python.

  If not installed, install it ...

• Make sure to have pip installed.

  Try: pip -V

  If it returns a path including /python3.x/, replace all the pip3 commands below by pip.

  If not installed, install it ...

• From PyPI

  • Install the latest version of mia_processes and its dependencies from the Python Packaging Index:

    pip3 install mia_processes # depending of the setup, it could be necessary to add --user option
    

• From source, for Linux distributions.

  • Install a Version Control System, for example git. Depending of your distribution, package management system can be different:

    sudo apt-get install git # Debian like
    sudo dnf install git # Fedora 22 and later
    # etc.
    

  • Clone the source codes.

    • Get source codes from Github. Replace [mia_processes_install_dir] with a directory of your choice:

      git clone https://github.com/populse/mia_processes.git [mia_processes_install_dir]
      

    • Or download the zip file (mia_processes-master.zip) of the project (green button "Clone or download"), then extract the data in the directory of your choice ([mia_processes_install_dir]):

      unzip mia_processes-master.zip -d [mia_processes_install_dir]  # In this case [mia_processes_install_dir] becomes [mia_processes_install_dir]/mia_processes-master
      

  • Install the Python module distribution:

    cd [mia_processes_install_dir]
    python3 setup.py install # depending of the setup, it could be necessary to add --user option
    

  • Remove the [mia_processes_install_dir] directory:

    cd ..
    rm -r [mia_install_dir]
    

• The populse project uses Git Large File Storage (LFS). In developer mode (without installing the source codes), after cloning the source codes, it is advisable to retrieve the large files with Git LFS:

  • If Git LFS is not already installed on your system, you need to install it first.

    • Ex. on Fedora:

      sudo dnf install git-lfs
      

  • Initialize Git LFS

    • On a reposirory:

      git lfs install
      

  • Retrieve Files with Git LFS

    • On a repository:

      git lfs pull
      

Third-party softwares

Many mia_processes bricks (atomic processes) use third-party softwares. To use these bricks, the corresponding third-party softwares must be installed.

Requirements

In order to get all the bricks and pipelines proposed by mia_processes some third libraries are required:

• boto
• cmp
• cfflib
• dipy
• nibabel
• nilearn
• nipy
• nipype
• nitime
• nitransforms
• numpy
• openpyxl
• paramiko
• populse-db >= 2.5.0, < 3.0.0
• populse_mia >= 2.5.0, < 3.0.0
• pyxnat
• reportlab
• scipy
• statsmodels
• templateflow
• torch
• vtk

License

• The whole populse project is open source.
• Mia_processes is precisely released under the CeCILL software license.
• All license details can be found here, or refer to the license file here.

Support and Communication

In case of a problem or to ask a question about how to do something in mia_processes, please open an issue.

The developer team can even be contacted using populse-support@univ-grenoble-alpes.fr.