Clone this repo:
git clone https://github.com/usc-mrel/PulseqT1T2Mapping.git
Navigate to the directory where its cloned.
Create the conda environment with the given "environment.yml" file.
conda env create -f environment.yml
Activate the environment:
conda activate pulseqmapping
Clone the pypulseq repository and switch to v140 branch:
git clone https://github.com/bilal-tasdelen/pypulseq.git
cd pypulseq
git checkout v140
Navigate to the directory before the cloned directory. Install pypulseq and its dependencies via pip:
pip install pypulseq/
Optionally install mplcursors from pip.
Optionall install python-bloch-simulator from https://github.com/utcsilab/bloch-simulator-python.
User inputs for the control of the scripts are given by user_opts.json. Currently user opts are consisting of:
show_diag: (bool) Whether or not to show sequence diagram.
write_seq: (bool) Whether or not to write the sequence to a file.
detailed_rep: (bool) Whether or not to generate a detailed report of the sequence. (Beware, its slow.)
param_filename: (string) Name of the protocol file to be used. File should be present under "protocols/".
Protocol parameters should be given in .json format. They can be found under "protocols/" directory. Protocol parameters can be following (subject to increase):
Common:
output_folder: (string) Directory name that sequence will be put into.
file_name: (string)
TE: (list of doubles) [secs]
TR: (double) [secs]
fov_inplane: (2 elements list of doubles) [m]
slice_thickness:
kz_os_steps:
matrix_size:
slice_orientation:
flip_angle:
exc_pulse_type:
slice_pos:
readout_duration:
Ndummy:
reset_block:
TBA
Currently there are following scripts:
- MultiEchoSpinEcho2D.py Implements a 2D MESE sequence to be used for T2 mapping.
- VariableFlipAngleGRE3D.py Implements a multi flip angle 3D Gre sequence to be used for B1 and T1 mapping.
- DesignBIR4.py Designs and simulates a BIR 4 pulse with given parameters, to be used in VFA-GRE B1 mapping.
- DesignSLR.py Designs and simulates an SLR pulse with given parameters, to be used in VFA-GRE.
- SliceProfile.py Simulates slice profiles of sinc and SLR pulses.
Non-exhaustive package list:
- Pypulseq (https://github.com/bilal-tasdelen/pypulseq/tree/v140)
- The original pypulseq repo has several bugs, especially for Pulseq 1.4.0, that makes these sequences non-functional. This repo includes bug fixes and small improvements over the original. Some of these commits are already a PR on the original repo, but adaptation of them takes time. In summary, sequences in this repo are only compatible with this fork.
- Sigpy (required by pypulseq)
- Matplotlib
- Numpy
- bloch-simulator-python (optional)
- Required for slice profile simulation and BIR-4 pulse simulation.
- Mplcursors (optional)
- Helps with debugging the sequence diagrams.
Dependencies are tested with conda. Environment exhaustive package list:
# Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
backcall 0.2.0 pypi_0 pypi
blas 1.0 mkl
brotli 1.0.9 h5eee18b_7
brotli-bin 1.0.9 h5eee18b_7
bzip2 1.0.8 h7b6447c_0
ca-certificates 2022.07.19 h06a4308_0
certifi 2022.6.15 py310h06a4308_0
cloudpickle 2.1.0 pypi_0 pypi
cycler 0.11.0 pyhd3eb1b0_0
dbus 1.13.18 hb2f20db_0
debugpy 1.6.3 pypi_0 pypi
decorator 5.1.1 pypi_0 pypi
entrypoints 0.4 pypi_0 pypi
expat 2.4.4 h295c915_0
fontconfig 2.13.1 h6c09931_0
fonttools 4.25.0 pyhd3eb1b0_0
freetype 2.11.0 h70c0345_0
giflib 5.2.1 h7b6447c_0
glib 2.69.1 h4ff587b_1
gst-plugins-base 1.14.0 h8213a91_2
gstreamer 1.14.0 h28cd5cc_2
icu 58.2 he6710b0_3
intel-openmp 2021.4.0 h06a4308_3561
ipykernel 6.15.1 pypi_0 pypi
ipython 7.34.0 pypi_0 pypi
jedi 0.18.1 pypi_0 pypi
jpeg 9e h7f8727e_0
jupyter-client 7.3.4 pypi_0 pypi
jupyter-core 4.11.1 pypi_0 pypi
kiwisolver 1.4.2 py310h295c915_0
krb5 1.19.2 hac12032_0
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.38 h1181459_1
lerc 3.0 h295c915_0
libbrotlicommon 1.0.9 h5eee18b_7
libbrotlidec 1.0.9 h5eee18b_7
libbrotlienc 1.0.9 h5eee18b_7
libclang 10.0.1 default_hb85057a_2
libdeflate 1.8 h7f8727e_5
libedit 3.1.20210910 h7f8727e_0
libevent 2.1.12 h8f2d780_0
libffi 3.3 he6710b0_2
libgcc-ng 11.2.0 h1234567_1
libgfortran-ng 7.5.0 ha8ba4b0_17
libgfortran4 7.5.0 ha8ba4b0_17
libgomp 11.2.0 h1234567_1
libllvm10 10.0.1 hbcb73fb_5
libpng 1.6.37 hbc83047_0
libpq 12.9 h16c4e8d_3
libstdcxx-ng 11.2.0 h1234567_1
libtiff 4.4.0 hecacb30_0
libuuid 1.0.3 h7f8727e_2
libwebp 1.2.2 h55f646e_0
libwebp-base 1.2.2 h7f8727e_0
libxcb 1.15 h7f8727e_0
libxkbcommon 1.0.1 hfa300c1_0
libxml2 2.9.14 h74e7548_0
libxslt 1.1.35 h4e12654_0
lz4-c 1.9.3 h295c915_1
matplotlib 3.5.2 pypi_0 pypi
matplotlib-inline 0.1.6 pypi_0 pypi
mkl 2021.4.0 h06a4308_640
mkl-service 2.4.0 py310h7f8727e_0
mkl_fft 1.3.1 py310hd6ae3a3_0
mkl_random 1.2.2 py310h00e6091_0
munkres 1.1.4 py_0
ncurses 6.3 h5eee18b_3
nest-asyncio 1.5.5 pypi_0 pypi
nspr 4.33 h295c915_0
nss 3.74 h0370c37_0
numpy 1.23.1 py310h1794996_0
numpy-base 1.23.1 py310hcba007f_0
openssl 1.1.1q h7f8727e_0
packaging 21.3 pyhd3eb1b0_0
parso 0.8.3 pypi_0 pypi
pcre 8.45 h295c915_0
pexpect 4.8.0 pypi_0 pypi
pickleshare 0.7.5 pypi_0 pypi
pillow 9.2.0 py310hace64e9_1
pip 22.1.2 py310h06a4308_0
ply 3.11 py310h06a4308_0
prompt-toolkit 3.0.30 pypi_0 pypi
psutil 5.9.1 pypi_0 pypi
ptyprocess 0.7.0 pypi_0 pypi
pygments 2.13.0 pypi_0 pypi
pyparsing 3.0.4 pyhd3eb1b0_0
pypulseq 1.4.0 pypi_0 pypi
pyqt 5.15.7 py310h6a678d5_1
pyqt5-sip 12.11.0 pypi_0 pypi
pyqtgraph 0.11.0 py_0
python 3.10.4 h12debd9_0
python-dateutil 2.8.2 pyhd3eb1b0_0
pyzmq 23.2.1 pypi_0 pypi
qt-main 5.15.2 h327a75a_7
qt-webengine 5.15.9 hd2b0992_4
qtwebkit 5.212 h4eab89a_4
readline 8.1.2 h7f8727e_1
scipy 1.8.1 pypi_0 pypi
setuptools 63.4.1 py310h06a4308_0
sip 6.6.2 py310h6a678d5_0
six 1.16.0 pyhd3eb1b0_1
spyder-kernels 2.3.2 pypi_0 pypi
sqlite 3.39.2 h5082296_0
tk 8.6.12 h1ccaba5_0
toml 0.10.2 pyhd3eb1b0_0
tornado 6.1 py310h7f8727e_0
traitlets 5.3.0 pypi_0 pypi
tzdata 2022a hda174b7_0
wcwidth 0.2.5 pypi_0 pypi
wheel 0.37.1 pyhd3eb1b0_0
wurlitzer 3.0.2 pypi_0 pypi
xz 5.2.5 h7f8727e_1
zlib 1.2.12 h7f8727e_2
zstd 1.5.2 ha4553b6_0
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