# mia_processes
<!-- [](https://codecov.io/github/populse/mia_processes) -->
[](https://github.com/populse/mia_processes/blob/master/LICENSE)
[](https://pypi.org/project/mia_processes/)
[](#)
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# Documentation
[The documentation is available in mia_processes's website](https://populse.github.io/mia_processes).
# Installation
* A compatible version of [Python](https://www.python.org/) (>= 3.5) and [pip](https://packaging.python.org/guides/tool-recommendations/) 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](https://docs.python.org/3/installing/index.html):
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](https://git-scm.com/book/en/v2/Getting-Started-About-Version-Control). Depending of your distribution, [package management system](https://en.wikipedia.org/wiki/Package_manager) 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"](https://github.com/populse/mia_processes)), 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](https://populse.github.io/populse_mia/html/installation/3rd-party_installations.html).
# 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](http://cecill.info/licences/Licence_CeCILL_V2.1-en.html), or refer to the license file [here](https://github.com/populse/mia_processes/blob/master/LICENSE).
# 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](https://github.com/populse/mia_processes/issues).
The developer team can even be contacted using populse-support@univ-grenoble-alpes.fr.
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