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@schuenke
schuenke authored Jan 8, 2025
2 parents 2ba91ce + 67d9994 commit b69cd49
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258 changes: 258 additions & 0 deletions pypulseq/seq_examples/notebooks/ESMRMB_DEMO_GRE_20211215.ipynb
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{
"nbformat": 4,
"nbformat_minor": 0,
"metadata": {
"colab": {
"name": "ESMRMB_DEMO_20211215.ipynb",
"provenance": [],
"collapsed_sections": [],
"toc_visible": true
},
"kernelspec": {
"name": "python3",
"display_name": "Python 3"
},
"language_info": {
"name": "python"
}
},
"cells": [
{
"cell_type": "markdown",
"source": [
"# **ESMRMB 2021 PyPulseq LIVE DEMO** - 12/15/2021"
],
"metadata": {
"id": "hc3VbKKCOidq"
}
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "AuVzrkgEaVTG"
},
"outputs": [],
"source": [
"!pip install pypulseq"
]
},
{
"cell_type": "code",
"source": [
"import pypulseq"
],
"metadata": {
"id": "hZqtcYtQXhGN"
},
"execution_count": null,
"outputs": []
},
{
"cell_type": "markdown",
"source": [
"### **IMPORT PACKAGES**"
],
"metadata": {
"id": "dXeeFq6Bc5-9"
}
},
{
"cell_type": "code",
"source": [
"import math\n",
"\n",
"import numpy as np\n",
"from matplotlib import pyplot as plt\n",
"\n",
"import pypulseq as pp"
],
"metadata": {
"id": "cwuaHdp_a8ub"
},
"execution_count": null,
"outputs": []
},
{
"cell_type": "markdown",
"source": [
"#### **SETUP**"
],
"metadata": {
"id": "qQ7uenQcdAWA"
}
},
{
"cell_type": "code",
"source": [
"# ======\n",
"# SETUP\n",
"# ======\n",
"# Create a new sequence object\n",
"seq = pp.Sequence()\n",
"\n",
"# Define FOV and resolution\n",
"fov = 256e-3\n",
"Nx = 256\n",
"Ny = 256\n",
"alpha = 10 # flip angle\n",
"slice_thickness = 3e-3 # slice\n",
"# TE = np.array([7.38]) * 1e-3 # give a vector here to have multiple TEs (e.g. for field mapping)\n",
"TE = np.array([4.3e-3])\n",
"TR = 10e-3\n",
"\n",
"rf_spoiling_inc = 117 # RF spoiling increment\n",
"\n",
"system = pp.Opts(max_grad=28, grad_unit='mT/m', max_slew=150, slew_unit='T/m/s', rf_ringdown_time=20e-6,\n",
" rf_dead_time=100e-6, adc_dead_time=10e-6)"
],
"metadata": {
"id": "EnvyC9kDbHwE"
},
"execution_count": null,
"outputs": []
},
{
"cell_type": "markdown",
"source": [
"#### **CREATE EVENTS**"
],
"metadata": {
"id": "JEUIGiM0dZqG"
}
},
{
"cell_type": "code",
"source": [
"# ======\n",
"# CREATE EVENTS\n",
"# ======\n",
"rf, gz, gzr = pp.make_sinc_pulse(flip_angle=alpha * math.pi / 180, duration=3e-3, slice_thickness=slice_thickness,\n",
" apodization=0.5, time_bw_product=4, system=system, return_gz=True)\n",
"# Define other gradients and ADC events\n",
"delta_k = 1 / fov\n",
"gx = pp.make_trapezoid(channel='x', flat_area=Nx * delta_k, flat_time=3.2e-3, system=system)\n",
"adc = pp.make_adc(num_samples=Nx, duration=gx.flat_time, delay=gx.rise_time, system=system)\n",
"gx_pre = pp.make_trapezoid(channel='x', area=-gx.area / 2, duration=1e-3, system=system)\n",
"gz_reph = pp.make_trapezoid(channel='z', area=-gz.area / 2, duration=1e-3, system=system)\n",
"phase_areas = (np.arange(Ny) - Ny / 2) * delta_k\n",
"\n",
"# gradient spoiling\n",
"gx_spoil = pp.make_trapezoid(channel='x', area=2 * Nx * delta_k, system=system)\n",
"gz_spoil = pp.make_trapezoid(channel='z', area=4 / slice_thickness, system=system)\n",
"\n",
"# Calculate timing\n",
"delay_TE = np.ceil((TE - pp.calc_duration(gx_pre) - gz.fall_time - gz.flat_time / 2 - pp.calc_duration(\n",
" gx) / 2) / seq.grad_raster_time) * seq.grad_raster_time\n",
"delay_TR = np.ceil((TR - pp.calc_duration(gz) - pp.calc_duration(gx_pre) - pp.calc_duration(\n",
" gx) - delay_TE) / seq.grad_raster_time) * seq.grad_raster_time\n",
"\n",
"assert np.all(delay_TE >= 0)\n",
"assert np.all(delay_TR >= pp.calc_duration(gx_spoil, gz_spoil))\n",
"\n",
"rf_phase = 0\n",
"rf_inc = 0\n"
],
"metadata": {
"id": "2TXWjpBkdVMm"
},
"execution_count": null,
"outputs": []
},
{
"cell_type": "markdown",
"source": [
"#### **CONSTRUCT SEQUENCE**"
],
"metadata": {
"id": "zBlSefhqdhix"
}
},
{
"cell_type": "code",
"source": [
"# ======\n",
"# CONSTRUCT SEQUENCE\n",
"# ======\n",
"# Loop over phase encodes and define sequence blocks\n",
"for i in range(Ny):\n",
" for j in range(len(TE)):\n",
" rf.phase_offset = rf_phase / 180 * np.pi\n",
" adc.phase_offset = rf_phase / 180 * np.pi\n",
" rf_inc = divmod(rf_inc + rf_spoiling_inc, 360.0)[1]\n",
" rf_phase = divmod(rf_phase + rf_inc, 360.0)[1]\n",
"\n",
" seq.add_block(rf, gz)\n",
" gy_pre = pp.make_trapezoid(channel='y', area=phase_areas[i], duration=pp.calc_duration(gx_pre), system=system)\n",
" seq.add_block(gx_pre, gy_pre, gz_reph)\n",
" seq.add_block(pp.make_delay(delay_TE[j]))\n",
" seq.add_block(gx, adc)\n",
" gy_pre.amplitude = -gy_pre.amplitude\n",
" seq.add_block(pp.make_delay(delay_TR[j]), gx_spoil, gy_pre, gz_spoil)"
],
"metadata": {
"id": "rOM1mAKfdb2t"
},
"execution_count": null,
"outputs": []
},
{
"cell_type": "markdown",
"source": [
"#### **VISUALIZE**"
],
"metadata": {
"id": "i5zQHVxadmTa"
}
},
{
"cell_type": "code",
"source": [
"# ======\n",
"# VISUALIZATION\n",
"# ======\n",
"seq.plot(time_range=[0, TR])"
],
"metadata": {
"id": "jI-QNyKkdpO7"
},
"execution_count": null,
"outputs": []
},
{
"cell_type": "markdown",
"source": [
"#### **DOWNLOAD `.SEQ` FILE**"
],
"metadata": {
"id": "YkctaLKud8uV"
}
},
{
"cell_type": "code",
"source": [
"from google.colab import files\n",
"\n",
"seq.write('esmrmb_demo_20211215.seq')\n",
"\n",
"files.download('esmrmb_demo_20211215.seq')"
],
"metadata": {
"id": "Kr1KW5JkdqcS"
},
"execution_count": null,
"outputs": []
},
{
"cell_type": "code",
"source": [
""
],
"metadata": {
"id": "l9IZS6R-eN_j"
},
"execution_count": null,
"outputs": []
}
]
}

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