OxfordASLRun
============

**Purpose.** Build and execute an ``oxford_asl`` command from ``data_descrip`` + ``params``.  
Handles ASL type (PCASL/PASL), TIs/PLDs, bolus, slice timing, structural usage, and calibration.

What it builds
--------------

- **Contrast ordering:** ``--iaf tc`` if ``LabelControl=True`` else ``--iaf ct``; default ``--ibf rpt`` (or as given).
- **Timing:** computes ``--tis`` (PLD+bolus) and ``--bolus`` from ``data_descrip`` for PCASL/PASL.
- **Acquisition:** adds ``--slicedt`` if ``SliceDuration`` is present.
- **Structural:** ``-s`` to anatomical when ``useStructural=True``.
- **Calibration:** if ``useCalibration=True``, supplies ``-c`` (M0), ``--tr`` and ``--alpha``.
- **Output:** sets ``-o <outdir>`` (defaults to derivatives mirror).
- **Execution:** runs with a controlled environment (``FSLOUTPUTTYPE=NIFTI_GZ``, single-thread OMP, locale-safe).

Inputs
------

- ``data_descrip`` with keys such as: ``ArterialSpinLabelingType``, ``PLDList``, ``LabelingDuration``,
  ``BolusCutOffDelayTime``, ``SliceDuration``, ``LabelControl``, ``Images`` (with ``asl`` and optional ``anat``/``M0``), etc.

Outputs
-------

- Returns ``{"oxford_asl_out": <outdir>}``. Oxford ASL result files are placed in ``<outdir>`` by the tool.

Configuration (``params``)
--------------------------

=================  ===================  ==========================================
Key                Type / Default       Meaning
=================  ===================  ==========================================
``wp``             bool / ``False``     White-paper mode (``--wp``)
``mc``             bool / ``False``     Motion correction (``--mc``)
``ibf``            str / ``rpt``        Intra-bolus format (with ``--iaf``)
``bat``            float / *None*       Priors (passed through as ``--bat``)
``t1``             float / *None*       Tissue T1 (``--t1``)
``t1b``            float / *None*       Blood T1 (``--t1b``)
``sliceband``      int / *None*         Slice banding (``--sliceband``)
``inferart``       bool / ``False``     ``--inferart``
``debug``          bool / ``False``     ``--debug``
``useStructural``  bool / ``False``     Add anatomical with ``-s``
``useCalibration`` bool / ``False``     Add M0 calibration (``-c``, ``--tr``, ``--alpha``)
``override_inputs`` dict / {}           Explicit ``asl_path`` / ``m0_path``
``outdir``         str / derivatives    Output directory
``env``            dict / {}            Extra environment vars during run
=================  ===================  ==========================================

YAML example
------------

.. code-block:: yaml

    modules:
      - name: OxfordASLRun
        params:
          wp: true
          mc: true
          useStructural: true
          useCalibration: true
          outdir: ./derivatives/oxasl_out