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DOC: Use the correct punctuation marks for et al.. #1484

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DOC: Use the correct punctuation marks for et al.. #1484

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20 changes: 10 additions & 10 deletions dipy/reconst/dsi.py
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Open in desktop
Expand Up @@ -32,7 +32,7 @@ def __init__(self,
where $\mathbf{r}$ is the displacement vector and $\mathbf{q}$ is the
wavector which corresponds to different gradient directions. Method
used to calculate the ODFs. Here we implement the method proposed by
Wedeen et. al [1]_.
Wedeen et al. [1]_.

The main assumption for this model is fast gradient switching and that
the acquisition gradients will sit on a keyhole Cartesian grid in
Expand All @@ -58,10 +58,10 @@ def __init__(self,

References
----------
.. [1] Wedeen V.J et. al, "Mapping Complex Tissue Architecture With
.. [1] Wedeen V.J et al., "Mapping Complex Tissue Architecture With
Diffusion Spectrum Magnetic Resonance Imaging", MRM 2005.

.. [2] Canales-Rodriguez E.J et. al, "Deconvolution in Diffusion
.. [2] Canales-Rodriguez E.J et al., "Deconvolution in Diffusion
Spectrum Imaging", Neuroimage, 2010.

.. [3] Garyfallidis E, "Towards an accurate brain tractography", PhD
Expand Down Expand Up @@ -217,13 +217,13 @@ def rtop_pdf(self, normalized=True):

References
----------
.. [1] Descoteaux M. et. al, "Multiple q-shell diffusion propagator
.. [1] Descoteaux M. et al., "Multiple q-shell diffusion propagator
imaging", Medical Image Analysis, vol 15, No. 4, p. 603-621, 2011.

.. [2] Tuch D.S., "Diffusion MRI of Complex Tissue Structure",
PhD Thesis, 2002.

.. [3] Wu Y. et. al, "Computation of Diffusion Function Measures
.. [3] Wu Y. et al., "Computation of Diffusion Function Measures
in q -Space Using Magnetic Resonance Hybrid Diffusion Imaging",
IEEE TRANSACTIONS ON MEDICAL IMAGING, vol. 27, No. 6, p. 858-865, 2008

Expand All @@ -246,7 +246,7 @@ def msd_discrete(self, normalized=True):
\end{equation}

where $\hat{\mathbf{r}}$ is a point in the 3D Propagator space
(see Wu et. al [1]_).
(see Wu et al. [1]_).

Parameters
----------
Expand All @@ -261,7 +261,7 @@ def msd_discrete(self, normalized=True):

References
----------
.. [1] Wu Y. et. al, "Hybrid diffusion imaging", NeuroImage, vol 36,
.. [1] Wu Y. et al., "Hybrid diffusion imaging", NeuroImage, vol 36,
p. 617-629, 2007.

"""
Expand Down Expand Up @@ -536,10 +536,10 @@ def __init__(self, gtab, qgrid_size=35, r_start=4.1, r_end=13.,

References
----------
.. [1] Canales-Rodriguez E.J et. al, "Deconvolution in Diffusion
.. [1] Canales-Rodriguez E.J et al., "Deconvolution in Diffusion
Spectrum Imaging", Neuroimage, 2010.

.. [2] Biggs David S.C. et. al, "Acceleration of Iterative Image
.. [2] Biggs David S.C. et al., "Acceleration of Iterative Image
Restoration Algorithms", Applied Optics, vol. 36, No. 8, p. 1766-1775,
1997.

Expand Down Expand Up @@ -626,7 +626,7 @@ def LR_deconv(prop, psf, numit=5, acc_factor=1):

References
----------
.. [1] Biggs David S.C. et. al, "Acceleration of Iterative Image
.. [1] Biggs David S.C. et al., "Acceleration of Iterative Image
Restoration Algorithms", Applied Optics, vol. 36, No. 8, p. 1766-1775,
1997.

Expand Down
8 changes: 4 additions & 4 deletions dipy/reconst/forecast.py
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Expand Up @@ -31,11 +31,11 @@ class ForecastModel(OdfModel, Cache):
Using High Angular Resolution Diffusion Imaging", Magnetic
Resonance in Medicine, 2005.

.. [2] Kaden E. et. al, "Quantitative Mapping of the Per-Axon Diffusion
.. [2] Kaden E. et al., "Quantitative Mapping of the Per-Axon Diffusion
Coefficients in Brain White Matter", Magnetic Resonance in
Medicine, 2016.

.. [3] Zucchelli E. et. al, "A generalized SMT-based framework for
.. [3] Zucchelli E. et al., "A generalized SMT-based framework for
Diffusion MRI microstructural model estimation", MICCAI Workshop
on Computational DIFFUSION MRI (CDMRI), 2017.
Notes
Expand Down Expand Up @@ -96,11 +96,11 @@ def __init__(self,
Using High Angular Resolution Diffusion Imaging", Magnetic
Resonance in Medicine, 2005.

.. [2] Kaden E. et. al, "Quantitative Mapping of the Per-Axon Diffusion
.. [2] Kaden E. et al., "Quantitative Mapping of the Per-Axon Diffusion
Coefficients in Brain White Matter", Magnetic Resonance in
Medicine, 2016.

.. [3] Zucchelli M. et. al, "A generalized SMT-based framework for
.. [3] Zucchelli M. et al., "A generalized SMT-based framework for
Diffusion MRI microstructural model estimation", MICCAI Workshop
on Computational DIFFUSION MRI (CDMRI), 2017.

Expand Down
4 changes: 2 additions & 2 deletions dipy/reconst/gqi.py
View file
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Expand Up @@ -33,7 +33,7 @@ def __init__(self,

References
----------
.. [1] Yeh F-C et. al, "Generalized Q-Sampling Imaging", IEEE TMI, 2010
.. [1] Yeh F-C et al., "Generalized Q-Sampling Imaging", IEEE TMI, 2010

.. [2] Garyfallidis E, "Towards an accurate brain tractography", PhD
thesis, University of Cambridge, 2012.
Expand Down Expand Up @@ -167,7 +167,7 @@ def squared_radial_component(x, tol=0.01):
def npa(self, odf, width=5):
""" non-parametric anisotropy

Nimmo-Smith et. al ISMRM 2011
Nimmo-Smith et al. ISMRM 2011
"""
# odf = self.odf(s)
t0, t1, t2 = triple_odf_maxima(self.odf_vertices, odf, width)
Expand Down
64 changes: 32 additions & 32 deletions dipy/reconst/mapmri.py
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Open in desktop
Expand Up @@ -39,15 +39,15 @@ class MapmriModel(ReconstModel, Cache):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.

.. [2] Ozarslan E. et. al, "Simple harmonic oscillator based reconstruction
.. [2] Ozarslan E. et al., "Simple harmonic oscillator based reconstruction
and estimation for one-dimensional q-space magnetic resonance
1D-SHORE)", eapoc Intl Soc Mag Reson Med, vol. 16, p. 35., 2008.

.. [3] Merlet S. et. al, "Continuous diffusion signal, EAP and ODF
.. [3] Merlet S. et al., "Continuous diffusion signal, EAP and ODF
estimation via Compressive Sensing in diffusion MRI", Medical
Image Analysis, 2013.

Expand Down Expand Up @@ -172,24 +172,24 @@ def __init__(self,

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.

.. [2] Ozarslan E. et. al, "Simple harmonic oscillator based
.. [2] Ozarslan E. et al., "Simple harmonic oscillator based
reconstruction and estimation for one-dimensional q-space
magnetic resonance 1D-SHORE)", eapoc Intl Soc Mag Reson Med,
vol. 16, p. 35., 2008.

.. [3] Ozarslan E. et. al, "Simple harmonic oscillator based
.. [3] Ozarslan E. et al., "Simple harmonic oscillator based
reconstruction and estimation for three-dimensional q-space
mri", ISMRM 2009.

.. [4] Fick, Rutger HJ, et al. "MAPL: Tissue microstructure estimation
using Laplacian-regularized MAP-MRI and its application to HCP
data." NeuroImage (2016).

.. [5] Merlet S. et. al, "Continuous diffusion signal, EAP and ODF
.. [5] Merlet S. et al., "Continuous diffusion signal, EAP and ODF
estimation via Compressive Sensing in diffusion MRI", Medical
Image Analysis, 2013.

Expand Down Expand Up @@ -497,7 +497,7 @@ def odf(self, sphere, s=2):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.
"""
Expand Down Expand Up @@ -527,7 +527,7 @@ def odf_sh(self, s=2):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.

Expand Down Expand Up @@ -556,7 +556,7 @@ def rtpp(self):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.

Expand Down Expand Up @@ -608,7 +608,7 @@ def rtap(self):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.

Expand Down Expand Up @@ -659,7 +659,7 @@ def rtop(self):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.

Expand Down Expand Up @@ -775,7 +775,7 @@ def ng(self):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.

Expand Down Expand Up @@ -803,7 +803,7 @@ def ng_parallel(self):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.

Expand Down Expand Up @@ -843,7 +843,7 @@ def ng_perpendicular(self):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.

Expand Down Expand Up @@ -976,7 +976,7 @@ def isotropic_scale_factor(mu_squared):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.
"""
Expand All @@ -1003,7 +1003,7 @@ def mapmri_index_matrix(radial_order):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.
"""
Expand Down Expand Up @@ -1031,7 +1031,7 @@ def b_mat(index_matrix):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.
"""
Expand Down Expand Up @@ -1063,7 +1063,7 @@ def b_mat_isotropic(index_matrix):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.
"""
Expand All @@ -1090,7 +1090,7 @@ def mapmri_phi_1d(n, q, mu):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.
"""
Expand Down Expand Up @@ -1120,7 +1120,7 @@ def mapmri_phi_matrix(radial_order, mu, q_gradients):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.
"""
Expand Down Expand Up @@ -1169,7 +1169,7 @@ def mapmri_psi_1d(n, x, mu):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.
"""
Expand All @@ -1196,7 +1196,7 @@ def mapmri_psi_matrix(radial_order, mu, rgrad):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.
"""
Expand Down Expand Up @@ -1244,7 +1244,7 @@ def mapmri_odf_matrix(radial_order, mu, s, vertices):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.
"""
Expand Down Expand Up @@ -1280,7 +1280,7 @@ def _odf_cfunc(n1, n2, n3, a, b, g, s):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.
"""
Expand Down Expand Up @@ -1321,7 +1321,7 @@ def mapmri_isotropic_phi_matrix(radial_order, mu, q):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.
"""
Expand Down Expand Up @@ -1361,7 +1361,7 @@ def mapmri_isotropic_radial_signal_basis(j, l, mu, qval):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.
"""
Expand Down Expand Up @@ -1437,7 +1437,7 @@ def mapmri_isotropic_psi_matrix(radial_order, mu, rgrad):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.
"""
Expand Down Expand Up @@ -1479,7 +1479,7 @@ def mapmri_isotropic_radial_pdf_basis(j, l, mu, r):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.
"""
Expand Down Expand Up @@ -1570,7 +1570,7 @@ def mapmri_isotropic_odf_matrix(radial_order, mu, s, vertices):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.

Expand Down Expand Up @@ -1628,7 +1628,7 @@ def mapmri_isotropic_odf_sh_matrix(radial_order, mu, s):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.

Expand Down Expand Up @@ -1731,7 +1731,7 @@ def mapmri_isotropic_index_matrix(radial_order):

References
----------
.. [1] Ozarslan E. et. al, "Mean apparent propagator (MAP) MRI: A novel
.. [1] Ozarslan E. et al., "Mean apparent propagator (MAP) MRI: A novel
diffusion imaging method for mapping tissue microstructure",
NeuroImage, 2013.
"""
Expand Down