.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "generated/gallery/13-fast-spin-echo/fse3D_adaptive.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_generated_gallery_13-fast-spin-echo_fse3D_adaptive.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_generated_gallery_13-fast-spin-echo_fse3D_adaptive.py:


========================================
Individually optimized 3D fast spin echo
========================================

Individually parameterized 3D FSE assigns different echo-train lengths and
repetition times to the shots that acquire central and peripheral k-space
[BUO25]_. From the central to the peripheral shots, TR and the minimum and
maximum angles of the refocusing schedule [BUS08b]_ follow a cubic
smooth-step transition between their two limits; the echo-train length
follows the same transition, rounded to integer values. The views are
assigned by an adaptive radial order. Longer trains and a different TR at the
periphery can reduce scan time, while the contrast at the centre of k-space
is set by the parameters of the central shots.

.. GENERATED FROM PYTHON SOURCE LINES 16-60

.. code-block:: Python


    from pypulseqpp import sequences

    Fse3DApp = sequences.fse3D_sequence.Fse3DApp

    P = {
        "n_x": 96,
        "n_y": 64,
        "n_z": 20,
        "fov_x": 0.20,
        "fov_y": 0.20,
        "fov_z": 0.12,
        "etl": 40,
        "etl_periphery": 72,
        "te": 200e-3,
        "tr": 1.2,
        "tr_periphery": 1.6,
        "refocusing_angle_deg": 120.0,
        "n_dummy": 0,
        "ordering": "radial",
        "flip_modulation": "optimized",
        "wave_amplitude": 0.0,
    }
    app = Fse3DApp(**P)
    seq = app.design()








.. GENERATED FROM PYTHON SOURCE LINES 61-72

Train parameters
----------------

TR and the schedule's minimum and maximum angles follow a cubic smooth-step
transition, :math:`3u^2 - 2u^3` with :math:`u` from 0 at the first (central)
shot to 1 at the last (peripheral) shot [BUO25]_; the echo-train length
follows the same transition rounded to integers. Every schedule passes
through the prescribed 120 degrees at the effective-TE echo. The schedules
of representative shots are plotted up to each shot's own train length:
the central shots reach lower minimum angles, and the peripheral shots have
shallower minima and longer trains.

.. GENERATED FROM PYTHON SOURCE LINES 72-95




.. image-sg:: /generated/gallery/13-fast-spin-echo/images/sphx_glr_fse3D_adaptive_001.png
   :alt: fse3D adaptive
   :srcset: /generated/gallery/13-fast-spin-echo/images/sphx_glr_fse3D_adaptive_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 96-105

Adaptive radial ordering
------------------------

The ordering ranks ``(shot, echo)`` slots jointly by distance from the
effective-TE echo and by position in the central-to-peripheral transition
[BUO25]_. Views are ranked by k-space radius; the innermost views fill the
slots nearest the effective-TE echo of the central shots, and within each group of one view per shot the views
are assigned to shots in order of angle. Colour gives the train length and
TR of the shot that acquired each view.

.. GENERATED FROM PYTHON SOURCE LINES 105-127




.. image-sg:: /generated/gallery/13-fast-spin-echo/images/sphx_glr_fse3D_adaptive_002.png
   :alt: fse3D adaptive
   :srcset: /generated/gallery/13-fast-spin-echo/images/sphx_glr_fse3D_adaptive_002.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 128-138

References
----------

.. [BUO25] Buonincontri G, et al. *Proceedings of the International Society
   for Magnetic Resonance in Medicine*. 2025; abstract 566-05-007.

.. [BUS08b] Busse RF, Brau ACS, Vu A, Michelich CR, Bayram E, Kijowski R,
   Reeder SB, Rowley HA. Effects of refocusing flip angle modulation and
   view ordering in 3D fast spin echo. *Magnetic Resonance in Medicine*.
   2008;60(3):640-649. https://doi.org/10.1002/mrm.21680


.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 4.112 seconds)


.. _sphx_glr_download_generated_gallery_13-fast-spin-echo_fse3D_adaptive.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: fse3D_adaptive.ipynb <fse3D_adaptive.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: fse3D_adaptive.py <fse3D_adaptive.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: fse3D_adaptive.zip <fse3D_adaptive.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_