.. _commandline:

Lyman Command-Line Interface
============================

The Nipype workflows for processing MRI data and estimating univariate models
are controlled through a set of command-line scripts, in concert with the
experiment and design information. For information about what these scripts do and how to use them, you can run ``<script_name> -h``. The help information is also reproduced on this page.

run_fmri.py
-----------

.. literalinclude:: commandline/run_fmri.txt

run_group.py
------------

.. literalinclude:: commandline/run_group.txt

run_warp.py
-----------

.. literalinclude:: commandline/run_warp.txt

make_masks.py
-------------

.. literalinclude:: commandline/make_masks.txt

anatomy_snapshots.py
--------------------

.. literalinclude:: commandline/anatomy_snapshots.txt

surface_snapshots.py
--------------------

.. literalinclude:: commandline/surface_snapshots.txt

view_ffx_results.py
-------------------

.. literalinclude:: commandline/view_ffx_results.txt