.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "generated/gallery/15-epi/epi2D_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_epi2D_sequence.py: ======================== 2D echo-planar imaging ======================== A slice-selective excitation is followed by alternating readout gradients and phase-encode blips that acquire multiple Cartesian lines in one echo train. Spoilers suppress residual transverse coherence between repetitions. Off-resonance phase accumulates during the train and produces geometric distortion along the phase-encode axis. EPI supports rapid structural imaging and functional MRI. .. GENERATED FROM PYTHON SOURCE LINES 13-93 .. GENERATED FROM PYTHON SOURCE LINES 94-100 Single-shot acquisition ----------------------- Every phase-encode line is acquired after one excitation. Echo-train length equals the number of acquired lines and determines the accumulated off-resonance phase across k-space. .. GENERATED FROM PYTHON SOURCE LINES 100-118 .. code-block:: Python from pypulseqpp.sequences import epi2D_sequence diagram = epi2D_sequence( n_x=64, n_y=48, n_slices=1, n_shots=1, n_dummy=0, fat_saturation=True, tr=None, ) single = epi2D_sequence(n_x=96, n_y=96, n_slices=1, n_shots=1, n_dummy=0) print( f"{diagram.num_blocks} blocks, {diagram.duration()[0] * 1e3:.1f} ms, " f"TE {diagram.get_definition('TE')[0] * 1e3:.2f} ms" ) .. rst-class:: sphx-glr-script-out .. code-block:: none 58 blocks, 50.6 ms, TE 22.14 ms .. GENERATED FROM PYTHON SOURCE LINES 119-121 Sequence diagram ---------------- .. GENERATED FROM PYTHON SOURCE LINES 121-124 .. code-block:: Python diagram.paper_plot() .. image-sg:: /generated/gallery/15-epi/images/sphx_glr_epi2D_sequence_001.png :alt: epi2D sequence :srcset: /generated/gallery/15-epi/images/sphx_glr_epi2D_sequence_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 125-138 Segmentation and in-plane acceleration -------------------------------------- Segmentation and in-plane acceleration both reduce echo-train length. ``n_shots`` interleaves the lines over several excitations, so every line is still acquired. ``ry`` skips lines within one excitation and requires a parallel-imaging reconstruction for the omitted lines. Off-resonance :math:`\Delta f` adds a phase of :math:`2\pi \Delta f\, \mathrm{esp}` per echo spacing :math:`\mathrm{esp}`. This phase is linear in :math:`k_y` and displaces the image along the phase-encode axis by :math:`\Delta f \cdot \mathrm{esp} \cdot N_\mathrm{etl}` pixels, where :math:`N_\mathrm{etl}` is the echo-train length. Both segmentation and acceleration reduce :math:`N_\mathrm{etl}` and therefore the displacement. .. GENERATED FROM PYTHON SOURCE LINES 138-163 .. code-block:: Python segmented = epi2D_sequence(n_x=96, n_y=96, n_slices=1, n_shots=3, n_dummy=0) accelerated = epi2D_sequence(n_x=96, n_y=96, n_slices=1, ry=3, n_dummy=0, n_acs_y=0) designs = {"1 shot": single, "3 shots": segmented, "ry = 3": accelerated} .. rst-class:: sphx-glr-script-out .. code-block:: none echoes trains per train TE (ms) scan (ms) px per Hz 1 shot 96 1 96.0 55.94 108.3 0.100 3 shots 96 3 32.0 23.46 131.6 0.035 ry = 3 32 1 32.0 23.44 43.1 0.035 .. GENERATED FROM PYTHON SOURCE LINES 164-171 Echo traversal -------------- The ordinate gives the phase-encode line acquired at each echo index. A single shot traverses the axis one line at a time. A segmented acquisition traverses it in steps of ``n_shots``, each shot starting one line further on. An accelerated acquisition traverses it once in steps of ``ry``. .. GENERATED FROM PYTHON SOURCE LINES 171-176 .. image-sg:: /generated/gallery/15-epi/images/sphx_glr_epi2D_sequence_002.png :alt: 1 shot, 3 shots, ry = 3 :srcset: /generated/gallery/15-epi/images/sphx_glr_epi2D_sequence_002.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 177-183 Which lines are acquired ------------------------ Segmentation and acceleration produce the same train length from different sets of lines: the segmented acquisition acquires every line, the accelerated acquisition one line in three. .. GENERATED FROM PYTHON SOURCE LINES 183-188 .. image-sg:: /generated/gallery/15-epi/images/sphx_glr_epi2D_sequence_003.png :alt: epi2D sequence :srcset: /generated/gallery/15-epi/images/sphx_glr_epi2D_sequence_003.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 189-196 Functional MRI time series --------------------------- Repeated frames form an fMRI time series. The acquisition below uses eight slices in four multiband groups. ``REP`` identifies the volume and ``SLC`` identifies the group; acquisition times are the start times of the ADC blocks in the sequence. .. GENERATED FROM PYTHON SOURCE LINES 196-228 .. code-block:: Python fmri = epi2D_sequence( n_x=64, n_y=64, n_slices=8, multiband=2, n_frames=4, n_shots=1, n_dummy=0, fat_saturation=False, tr=1.0, ) labels = fmri.evaluate_labels(evolution="adc") .. image-sg:: /generated/gallery/15-epi/images/sphx_glr_epi2D_sequence_004.png :alt: epi2D sequence :srcset: /generated/gallery/15-epi/images/sphx_glr_epi2D_sequence_004.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 0.848 seconds) .. _sphx_glr_download_generated_gallery_15-epi_epi2D_sequence.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: epi2D_sequence.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: epi2D_sequence.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: epi2D_sequence.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_