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DOC: Hyperlink DOIs to preferred resolver #2833

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Hyperlink DOIs to preferred resolver
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@katrinleinweber
katrinleinweber committedDec 19, 2018
commit 8871904c76d97140fb684047e6bd0601c25fb624
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Expand Up@@ -271,7 +271,7 @@ class FramewiseDisplacement(BaseInterface):
.. [Power2012] Power et al., Spurious but systematic correlations in functional
connectivity MRI networks arise from subject motion, NeuroImage 59(3),
2012. doi:`10.1016/j.neuroimage.2011.10.018
<http://dx.doi.org/10.1016/j.neuroimage.2011.10.018>`_.
<https://doi.org/10.1016/j.neuroimage.2011.10.018>`_.


"""
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Expand Up@@ -1587,7 +1587,7 @@ class KellyKapowski(ANTSCommand):
"year={2009},"
"issn={1053-8119},"
"url={http://www.sciencedirect.com/science/article/pii/S1053811908012780},"
"doi={http://dx.doi.org/10.1016/j.neuroimage.2008.12.016}"
"doi={https://doi.org/10.1016/j.neuroimage.2008.12.016}"
"}"),
'description':
'The details on the implementation of DiReCT.',
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Expand Up@@ -123,7 +123,7 @@ class Denoise(DipyBaseInterface):

.. [Coupe2008] Coupe P et al., `An Optimized Blockwise Non Local Means
Denoising Filter for 3D Magnetic Resonance Images
<http://dx.doi.org/10.1109%2FTMI.2007.906087>`_,
<https://doi.org/10.1109%2FTMI.2007.906087>`_,
IEEE Transactions on Medical Imaging, 27(4):425-441, 2008.


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Expand Up@@ -288,7 +288,7 @@ def _compute_voxel(args):
.. [Alexander2002] Alexander et al., Detection and modeling of non-Gaussian
apparent diffusion coefficient profiles in human brain data, MRM
48(2):331-340, 2002, doi: `10.1002/mrm.10209
<http://dx.doi.org/10.1002/mrm.10209>`_.
<https://doi.org/10.1002/mrm.10209>`_.
.. [Pierpaoli1996] Pierpaoli et al., Diffusion tensor MR imaging
of the human brain, Radiology 201:637-648. 1996.
"""
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Expand Up@@ -139,7 +139,7 @@ class SpaceTimeRealigner(NipyBaseInterface):
application to joint correction of motion and slice timing \
in fMRI. IEEE Trans Med Imaging. 2011 Aug;30(8):1546-54. DOI_.
.. _DOI: http://dx.doi.org/10.1109/TMI.2011.2131152
.. _DOI: https://doi.org/10.1109/TMI.2011.2131152
"""

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Expand Up@@ -164,7 +164,7 @@ class PETPVC(CommandLine):
"number={22},"
"pages={7975},"
"url={http://stacks.iop.org/0031-9155/61/i=22/a=7975},"
"doi={http://dx.doi.org/10.1088/0031-9155/61/22/7975},"
"doi={https://doi.org/10.1088/0031-9155/61/22/7975},"
"year={2016},"
"}"),
'description':
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Expand Up@@ -388,12 +388,12 @@ def hmc_pipeline(name='motion_correct'):

.. [Leemans09] Leemans A, and Jones DK, `The B-matrix must be rotated
when correcting for subject motion in DTI data
<http://dx.doi.org/10.1002/mrm.21890>`_,
<https://doi.org/10.1002/mrm.21890>`_,
Magn Reson Med. 61(6):1336-49. 2009. doi: 10.1002/mrm.21890.

.. [Yendiki13] Yendiki A et al., `Spurious group differences due to head
motion in a diffusion MRI study
<http://dx.doi.org/10.1016/j.neuroimage.2013.11.027>`_.
<https://doi.org/10.1016/j.neuroimage.2013.11.027>`_.
Neuroimage. 21(88C):79-90. 2013. doi: 10.1016/j.neuroimage.2013.11.027

Example
Expand DownExpand Up@@ -656,11 +656,11 @@ def sdc_fmb(name='fmb_correction',

.. [Jezzard95] Jezzard P, and Balaban RS, `Correction for geometric
distortion in echo planar images from B0 field variations
<http://dx.doi.org/10.1002/mrm.1910340111>`_,
<https://doi.org/10.1002/mrm.1910340111>`_,
MRM 34(1):65-73. (1995). doi: 10.1002/mrm.1910340111.

.. [Jenkinson03] Jenkinson M., `Fast, automated, N-dimensional
phase-unwrapping algorithm <http://dx.doi.org/10.1002/mrm.10354>`_,
phase-unwrapping algorithm <https://doi.org/10.1002/mrm.10354>`_,
MRM 49(1):193-197, 2003, doi: 10.1002/mrm.10354.

"""
Expand DownExpand Up@@ -873,7 +873,7 @@ def sdc_peb(name='peb_correction',

.. [Andersson2003] Andersson JL et al., `How to correct susceptibility
distortions in spin-echo echo-planar images: application to diffusion
tensor imaging <http://dx.doi.org/10.1016/S1053-8119(03)00336-7>`_.
tensor imaging <https://doi.org/10.1016/S1053-8119(03)00336-7>`_.
Neuroimage. 2003 Oct;20(2):870-88. doi: 10.1016/S1053-8119(03)00336-7

.. [Cordes2000] Cordes D et al., Geometric distortion correction in EPI
Expand DownExpand Up@@ -951,7 +951,7 @@ def remove_bias(name='bias_correct'):

.. [Jeurissen2014] Jeurissen B. et al., `Multi-tissue constrained
spherical deconvolution for improved analysis of multi-shell diffusion
MRI data <http://dx.doi.org/10.1016/j.neuroimage.2014.07.061>`_.
MRI data <https://doi.org/10.1016/j.neuroimage.2014.07.061>`_.
NeuroImage (2014). doi: 10.1016/j.neuroimage.2014.07.061


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