.. include:: links.rst

------------
Installation
------------
*fMRIPost-AROMA* should be installed using container technologies.

.. code-block:: bash
  docker pull nipreps/fmripost-aroma:main


Containerized execution (Docker and Singularity)
================================================
*fMRIPost-AROMA* is a *NiPreps* application, and therefore follows some overarching principles
of containerized execution drawn from the BIDS-Apps protocols.
For detailed information of containerized execution of *NiPreps*, please visit the corresponding
`Docker <https://www.nipreps.org/apps/docker/>`__
or `Singularity <https://www.nipreps.org/apps/singularity/>`__ subsections.

External Dependencies
---------------------
*fMRIPost-AROMA* is written using Python 3.8 (or above), and is based on
nipype_.

*fMRIPost-AROMA* requires some other neuroimaging software tools that are
not handled by the Python's packaging system (Pypi):

- FSL_ (version 6.0.7.7)
- ANTs_ (version 2.5.1)
- AFNI_ (version 24.0.05)
- `C3D <https://sourceforge.net/projects/c3d/>`_ (version 1.4.0)
- FreeSurfer_ (version 7.3.2)
- `bids-validator <https://github.com/bids-standard/bids-validator>`_ (version 1.14.0)
- `connectome-workbench <https://www.humanconnectome.org/software/connectome-workbench>`_ (version 1.5.0)

Not running on a local machine? - Data transfer
===============================================
If you intend to run *fMRIPost-AROMA* on a remote system, you will need to
make your data available within that system first.

For instance, here at the Poldrack Lab we use Stanford's
:abbr:`HPC (high-performance computing)` system, called Sherlock.
Sherlock enables `the following data transfer options
<https://www.sherlock.stanford.edu/docs/user-guide/storage/data-transfer/>`_.

Alternatively, more comprehensive solutions such as `Datalad
<https://www.datalad.org/>`_ will handle data transfers with the appropriate
settings and commands.
Datalad also performs version control over your data.