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mia_processes

Project description

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

  • 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.

Project details


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