.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "generated/gallery/15-epi/epi3D_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_15-epi_epi3D_sequence.py: ======================== 3D echo-planar imaging ======================== A slab-selective excitation is followed by alternating readout gradients with phase-encode and partition blips. The sampled ``(line, partition)`` views form a CAIPIRINHA lattice [BRE06]_, and segmented skipped-CAIPI traversal [STI21]_ distributes the lattice among shots. Spoilers suppress residual transverse coherence between repetitions; off-resonance accumulates during each echo train. 3D EPI supports rapid structural and functional imaging. .. GENERATED FROM PYTHON SOURCE LINES 13-144 .. GENERATED FROM PYTHON SOURCE LINES 145-152 Accelerated acquisition ----------------------- The first configuration uses in-plane and partition acceleration, three shots per shell, and a nonzero CAIPI shift. Each shot reads every third sampled lattice line; successive echoes therefore contain both the skipped-line displacement and the partition jump. .. GENERATED FROM PYTHON SOURCE LINES 152-171 .. code-block:: Python from pypulseqpp.sequences import epi3D_sequence baseline = epi3D_sequence( n_x=64, n_y=64, n_z=16, ry=2, rz=4, n_shots=3, n_dummy=0, ) print(f"{baseline.num_blocks} blocks, {baseline.duration()[0]:.2f} s") print( f"CAIPI shift {int(baseline.get_definition('CaipiShift')[0])}, " f"TE {baseline.get_definition('TE')[0] * 1e3:.2f} ms, " f"TR {baseline.get_definition('TR')[0] * 1e3:.1f} ms" ) .. rst-class:: sphx-glr-script-out .. code-block:: none 228 blocks, 0.19 s CAIPI shift 2, TE 8.83 ms, TR 189.4 ms .. GENERATED FROM PYTHON SOURCE LINES 172-174 Sequence diagram ---------------- .. GENERATED FROM PYTHON SOURCE LINES 174-177 .. code-block:: Python baseline.paper_plot() .. image-sg:: /generated/gallery/15-epi/images/sphx_glr_epi3D_sequence_001.png :alt: epi3D sequence :srcset: /generated/gallery/15-epi/images/sphx_glr_epi3D_sequence_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 178-192 Skipped-CAIPI traversal ----------------------- Each cell of the lattice is one ``(line, partition)`` view, shaded where it is sampled. Lines and arrows connect consecutive echoes within each train. No line joins separate shots. The panel title gives the pattern as :math:`S \cdot (R_y \times R_z)_{z\Delta z}`, with accelerations :math:`R_y` and :math:`R_z`, segmentation factor :math:`S` (shots per shell) and CAIPI shift :math:`\Delta z` as defined in [STI21]_. The partition jumps between consecutive echoes are the CAIPI blips: they alternate between amplitudes :math:`b^{(1)} = (S \cdot \Delta z) \bmod R_z` and :math:`b^{(2)} = (R_z - b^{(1)}) \bmod R_z` partitions, and the pattern repeats every :math:`n` echoes. Equivalent shells are folded onto one lattice cell; a small vertical display offset separates coincident paths from different shots. .. GENERATED FROM PYTHON SOURCE LINES 192-199 .. image-sg:: /generated/gallery/15-epi/images/sphx_glr_epi3D_sequence_002.png :alt: $3\cdot{2\times4}_{z2}$: $b^{(1)}=2,\ b^{(2)}=2,\ n=2$ :srcset: /generated/gallery/15-epi/images/sphx_glr_epi3D_sequence_002.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 200-208 Single-shot comparison ---------------------- With ``n_shots=1``, one longer echo train acquires the same lattice for each shell. Three shots shorten each echo train and therefore the geometric distortion along the phase-encode axis. The phase-encode step between consecutive echoes of a segmented train spans three sampled lattice lines, so its blips are larger than those of the single-shot train. .. GENERATED FROM PYTHON SOURCE LINES 208-245 .. code-block:: Python single_shot = epi3D_sequence( n_x=64, n_y=64, n_z=16, ry=2, rz=4, n_shots=1, n_dummy=0, ) .. image-sg:: /generated/gallery/15-epi/images/sphx_glr_epi3D_sequence_003.png :alt: $3\cdot{2\times4}_{z2}$: $b^{(1)}=2,\ b^{(2)}=2,\ n=2$, $1\cdot{2\times4}_{z2}$: $b^{(1)}=2,\ b^{(2)}=2,\ n=2$ :srcset: /generated/gallery/15-epi/images/sphx_glr_epi3D_sequence_003.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none echoes trains per train TE (ms) 3 shots 120 12 10.0 8.83 1 shot 128 4 32.0 17.10 .. GENERATED FROM PYTHON SOURCE LINES 246-253 In-plane acceleration --------------------- ``ry`` subsamples phase-encode lines, reducing echo-train length and increasing lattice spacing along :math:`k_y`. The sampled views remain on a single CAIPIRINHA lattice, whose CAIPI shift determines the positions of the aliases [BRE06]_. .. GENERATED FROM PYTHON SOURCE LINES 253-274 .. code-block:: Python accelerated = epi3D_sequence( n_x=64, n_y=64, n_z=16, ry=3, rz=2, n_shots=3, n_dummy=0, ) print( f"ry=3, rz=2: CAIPI shift {int(accelerated.get_definition('CaipiShift')[0])}, " f"{accelerated.num_blocks} blocks, {accelerated.duration()[0]:.2f} s" ) .. image-sg:: /generated/gallery/15-epi/images/sphx_glr_epi3D_sequence_004.png :alt: $3\cdot{3\times2}_{z1}$: $b^{(1)}=1,\ b^{(2)}=1,\ n=2$ :srcset: /generated/gallery/15-epi/images/sphx_glr_epi3D_sequence_004.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none ry=3, rz=2: CAIPI shift 1, 384 blocks, 0.32 s .. GENERATED FROM PYTHON SOURCE LINES 275-287 References ---------- .. [BRE06] Breuer FA, Blaimer M, Mueller MF, Seiberlich N, Heidemann RM, Griswold MA, Jakob PM. Controlled aliasing in volumetric parallel imaging (2D CAIPIRINHA). *Magnetic Resonance in Medicine*. 2006;55(3):549-556. https://doi.org/10.1002/mrm.20787 .. [STI21] Stirnberg R, Stöcker T. Segmented K-space blipped-controlled aliasing in parallel imaging for high spatiotemporal resolution EPI. *Magnetic Resonance in Medicine*. 2021;85(3):1540-1551. https://doi.org/10.1002/mrm.28486 .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 0.561 seconds) .. _sphx_glr_download_generated_gallery_15-epi_epi3D_sequence.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: epi3D_sequence.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: epi3D_sequence.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: epi3D_sequence.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_