Metadata-Version: 1.2
Name: ssfp
Version: 0.5.0
Summary: SSFP simulation
Home-page: https://github.com/mckib2/ssfp
Author: Nicholas McKibben
Author-email: nicholas.bgp@gmail.com
License: GPLv3
Description: 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()`
        - 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
        
            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 = 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
        
        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.
        
Platform: UNKNOWN
Requires-Python: >=3.5
