Introduction Part IV - Parametric Definitions

Building on the core functionality, cmrseq includes a library of parameterized definitions for commonly occuring groups of building blocks.

This notebooks highlights a few deinitions to demonstrate the principle of usage.

A full list of implemented definitions is given in the API Documentation

Imports

from copy import deepcopy

import numpy as np
from pint import Quantity
import matplotlib.pyplot as plt

import sys
sys.path.insert(0, "../../..")
import cmrseq

Define System Specs

system_specs = cmrseq.SystemSpec(gamma=Quantity(42.575, "MHz/T"),
                                 grad_raster_time=Quantity(5, "us"),
                                 max_grad=Quantity(40, "mT/m"),
                                 max_slew=Quantity(120, "mT/m/ms"),
                                 rf_raster_time=Quantity(5, "us"),
                                 adc_raster_time=Quantity(0.1, "us"))

Slice Selective Excitation

Returns a single sequence object containing gradients and an RF pulse

slice_selective_rf = cmrseq.seqdefs.excitation.slice_selective_sinc_pulse(system_specs,
                                                                          slice_thickness=Quantity(10, "mm"),
                                                                          flip_angle=Quantity(90, "degree"),
                                                                          pulse_duration=Quantity(0.8, "ms"),
                                                                          time_bandwidth_product=4,
                                                                          delay=Quantity(0, "ms"),
                                                                          slice_normal=np.array([0., 0., 1.]),
                                                                          slice_position_offset=Quantity(5, "cm"))
fig, ax = plt.subplots(1, 1, figsize=(18, 4))
cmrseq.plotting.plot_sequence(slice_selective_rf, axes=ax)
fig.suptitle(f"Slice Selective excitation \n {slice_selective_rf.blocks}n")
fig.tight_layout()

EPI Readout

epi_readout = cmrseq.seqdefs.readout.single_shot_epi(system_specs, field_of_view=Quantity([20, 20], "cm"), matrix_size=np.array([101, 11]),
                                                    blip_direction="up", partial_fourier_lines=3, slope_sampling=True, water_fat_shift='maximum',
                                                    max_total_duration=Quantity(35, "ms"))


figure = plt.figure(figsize=(16, 8))
axes = figure.subplot_mosaic("AAB;CCC")
axes = np.array([axes[k] for k in "ABC"])

cmrseq.plotting.plot_sequence(seq=epi_readout, axes=axes[0], plot_center_lines=True)
cmrseq.plotting.plot_kspace_2d(seq=epi_readout, k_axes=(0, 1), ax=axes[1])
cmrseq.plotting.plot_block_names(seq=epi_readout, axis=axes[2], fontsize=8)
figure.tight_layout()

Balanced steady state free precession (BSSFP)

bssfp_list = cmrseq.seqdefs.sequences.balanced_ssfp(system_specs,
                                                    inplane_resolution=Quantity([2, 2], "mm"),
                                                    matrix_size=np.array([51, 51]),
                                                    slice_thickness=Quantity(10, "mm"),
                                                    adc_duration=Quantity(0.5, "ms"),
                                                    flip_angle=Quantity(30, "degree"),
                                                    pulse_duration=Quantity(0.8, "ms"),
                                                    repetition_time=Quantity(0, "ms"),
                                                    dummy_shots=10)
bssfp = bssfp_list[0]
bssfp.extend(bssfp_list[1:20])

fig, ax = plt.subplots(1, 1, figsize=(18, 4))
cmrseq.plotting.plot_sequence(bssfp, axes=ax)
fig.suptitle("BSSFP TR 1-20")
fig.tight_layout()

/opt/conda/lib/python3.10/site-packages/pint/facets/plain/quantity.py:1345: RuntimeWarning: invalid value encountered in double_scalars
  magnitude = magnitude_op(new_self._magnitude, other._magnitude)
/mnt/code/cmrseq/docs/source/getting_started/../../../cmrseq/parametric_definitions/sequences/_ssfp.py:129: UserWarning: Repetition time too short to be feasible, set TR to 3.06 millisecond
  warn(f"Repetition time too short to be feasible, set TR to {minimal_tr}")
Extending Sequence: 100%|███████████████████████████████████████████████████████████████████| 19/19 [00:00<00:00, 252.07it/s]