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 can be use 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]
    

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.