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https://github.com/mckib2/ssfp

SSFP simulation and algorithms.
https://github.com/mckib2/ssfp

bssfp mri ssfp

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SSFP simulation and algorithms.

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README 

        
SSFP

====



Simple steady-state free precession simulation.  The goal is to

provide a simple to use, pip-installable solution for simulating and

working with this wonderful pulse sequence.



In this package:



- bSSFP: `bssfp()`

- FIMTRE: `fimtre()`

- GRE: `gre()`

- GS solution: `gs_recon()`

- PLANET: `planet()`

- 3D Region Growing Phase Correction: `rgphcorr3d()`

- Robust Coil Combination: `robustcc()`



Installation

============



Should be as easy as:



.. code-block:: bash



    python -m pip install ssfp



Usage

=====



See `ssfp.examples` for typical usage.  You can run examples like:



.. code-block:: bash



    python -m ssfp.examples.basic_bssfp



Balanced steady-state free precession can be called through `bssfp()`.

This is an implementation of equations [1--2] in [1]_.  These

equations are based on the Ernst-Anderson derivation [2]_ where

off-resonance is assumed to be subtracted as opposed to added (as in

the Freeman-Hill derivation [3]_).  Hoff actually gets Mx and My

flipped in the paper, so we fix that here.  We also assume that

the field map will be provided given the Freeman-Hill convention.



.. code-block:: python



    from ssfp import bssfp



    # Here's the simplest usage, see docstring for all the possible

    # function arguments

    sig = bssfp(T1, T2, TR, alpha)



We can also easily get the Geometric Solution to the elliptical

signal model as described in [1]_ as follows:



.. code-block:: python



    from ssfp import gs_recon

    recon = gs_recon(phased_cycled_images, pc_axis=-1)



    # Notice that we can specify the axis where the phase-cycles live



PLANET [4]_ is a method for simultaneous T1, T2 fitting for bSSFP

phase-cycled data.  Call like this:



.. code-block:: python



    from ssfp import planet



    # For a single pixel:

    Meff, T1, T2, df = planet(

        phased_cycled_pixels, alpha, TR, T1_guess,

        pcs=np.deg2rad([0, 90, 180, 270, etc...]))



3D Region Growing Phase Correction [5]_ is an algorithm for

determining water and fat images from a single bSSFP acquisition.

It can be called like this:



.. code-block:: python



    from ssfp import rgphcorr3d

    phase_corrected = rgphcorr3d(

        dataset3d, cellsize=(4, 4, 4), slice_axis=-1)



    # see ssfp.examples.basic_rgphcorr for full usage example



Robust Coil Combination for bSSFP Elliptical Signal Model [6]_ is a

coil combination method that preserves the elliptical relationships

between phase-cycled pixels.  It has two variants: simple and full.

By default, the simple method is called.  The full method is very

slow and only used for validation of the simple method.

Robust coil combination can be called like this:



.. code-block:: python



    from ssfp import robustcc



    sx, sy, sz, num_pc, num_coils = data.shape[:]

    coil_combined = robustcc(data, pc_axis=-2, coil_axis=-1)



    # see ssfp.examples.basic_robustcc for more usage examples



Changelog

=========



- 1.2.0: setup.py -> pyproject.toml; GPL -> MIT licence; general maintenance;

  dependency version bumps; type annotations; divide-by-zero fixes

- 1.0.0: `bssfp()` function overhaul to allow arbitrarily dimensioned

  input arrays or scalars and removes the `target_pc_axis` argument.



References

==========

.. [1] Xiang, Qing‐San, and Michael N. Hoff. "Banding artifact

       removal for bSSFP imaging with an elliptical signal

       model." Magnetic resonance in medicine 71.3 (2014):

       927-933.

.. [2] Ernst, Richard R., and Weston A. Anderson. "Application of

       Fourier transform spectroscopy to magnetic resonance."

       Review of Scientific Instruments 37.1 (1966): 93-102.

.. [3] Freeman R, Hill H. Phase and intensity anomalies in

       fourier transform NMR. J Magn Reson 1971;4:366–383.

.. [4] Shcherbakova, Yulia, et al. "PLANET: an ellipse fitting

       approach for simultaneous T1 and T2 mapping using

       phase‐cycled balanced steady‐state free precession."

       Magnetic resonance in medicine 79.2 (2018): 711-722.

.. [5] Hargreaves, Brian A., et al. "Fat‐suppressed steady‐state

       free precession imaging using phase detection." Magnetic

       Resonance in Medicine: An Official Journal of the

       International Society for Magnetic Resonance in Medicine

       50.1 (2003): 210-213.

.. [6] N. McKibben, G. Tarbox, E. DiBella, and N. K. Bangerter,

       "Robust Coil Combination for bSSFP Elliptical Signal

       Model," Proceedings of the 28th Annual Meeting of the

       ISMRM; Sydney, NSW, Australia, 2020.