.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "generated/gallery/12-mprage/mprage3D_sequence.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_generated_gallery_12-mprage_mprage3D_sequence.py: ==================== 3D Cartesian MPRAGE ==================== An inversion preparation is followed after the prescribed inversion delay by a train of low-flip-angle spoiled Cartesian gradient echoes. The inversion time is measured to the first excitation centre; the corresponding central ADC sample occurs one TE later. The ordering assigns recovery times within each inversion cycle to ``(line, partition)`` views. MPRAGE is used for high-resolution 3D T1-weighted structural imaging. .. GENERATED FROM PYTHON SOURCE LINES 13-69 .. GENERATED FROM PYTHON SOURCE LINES 70-79 Timing structure ---------------- Each cycle comprises inversion, crusher, inversion delay, spoiled gradient-echo train and recovery interval. ``ti=None`` and ``tr=None`` take the shortest inversion time and recovery supported by the modules. Four lines per partition provide a compact timing diagram. Clinical matrices typically require inversion times of several hundred milliseconds and much longer readout trains. .. GENERATED FROM PYTHON SOURCE LINES 79-89 .. code-block:: Python from pypulseqpp.sequences import mprage3D_sequence compact = mprage3D_sequence(n_x=128, n_y=4, n_z=4, ti=None, tr=None, n_dummy=0) print( f"{compact.num_blocks} blocks, {compact.duration()[0]:.2f} s, " f"TI {compact.get_definition('TI')[0] * 1e3:.0f} ms, " f"TR {compact.get_definition('TR')[0] * 1e3:.0f} ms" ) .. rst-class:: sphx-glr-script-out .. code-block:: none 80 blocks, 0.16 s, TI 8 ms, TR 41 ms .. GENERATED FROM PYTHON SOURCE LINES 90-92 .. code-block:: Python compact.paper_plot() .. image-sg:: /generated/gallery/12-mprage/images/sphx_glr_mprage3D_sequence_001.png :alt: mprage3D sequence :srcset: /generated/gallery/12-mprage/images/sphx_glr_mprage3D_sequence_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 93-104 Sampling order -------------- At a protocol matrix, each inversion cycle acquires the sampled lines of one partition: the inversion cycle is constant along each row of the map, and the index within the train runs outward from the centre of the line axis. The centre of k-space is therefore the first view in a train. ``TI`` is measured from the inversion-pulse centre to that view's excitation-pulse centre; the central ADC sample occurs one echo time later, at ``TI + TE``. Peripheral lines are acquired later in the recovery. .. GENERATED FROM PYTHON SOURCE LINES 104-117 .. code-block:: Python protocol = mprage3D_sequence(n_x=192, n_y=128, n_z=24, ti=0.9, tr=2.3, n_dummy=0) print( f"{protocol.duration()[0]:.1f} s, " f"{int(np.asarray(protocol.evaluate_labels(evolution='adc')['ECO']).max()) + 1} " "readouts in the longest train, " f"central ADC at {(protocol.get_definition('TI')[0] + protocol.get_definition('TE')[0]) * 1e3:.1f} ms" ) .. image-sg:: /generated/gallery/12-mprage/images/sphx_glr_mprage3D_sequence_002.png :alt: mprage3D sequence :srcset: /generated/gallery/12-mprage/images/sphx_glr_mprage3D_sequence_002.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none 55.2 s, 128 readouts in the longest train, central ADC at 904.0 ms .. GENERATED FROM PYTHON SOURCE LINES 118-127 Accelerated sampling -------------------- ``ry`` and ``rz`` subsample the line and partition axes. ``caipi_shift`` offsets the sampled partitions between adjacent lines to control the alias distribution. Fewer lines per partition reduce both train duration and the range of inversion-recovery weighting. Scan duration equals the number of inversion cycles multiplied by TR; the fully sampled calibration region still requires every partition. .. GENERATED FROM PYTHON SOURCE LINES 127-143 .. code-block:: Python accelerated = mprage3D_sequence( n_x=192, n_y=128, n_z=24, ry=2, rz=2, caipi_shift=1, ti=0.9, tr=2.3, n_dummy=0 ) .. image-sg:: /generated/gallery/12-mprage/images/sphx_glr_mprage3D_sequence_003.png :alt: mprage3D sequence :srcset: /generated/gallery/12-mprage/images/sphx_glr_mprage3D_sequence_003.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none views cycles per train scan (s) 1 x 1 2391 24 99.6 55.2 2 x 2, shift 1 883 24 36.8 55.2 .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 0.852 seconds) .. _sphx_glr_download_generated_gallery_12-mprage_mprage3D_sequence.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: mprage3D_sequence.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: mprage3D_sequence.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: mprage3D_sequence.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_