diff --git a/doc/about.rst b/doc/about.rst index 8809b35a34..f9d2831f70 100644 --- a/doc/about.rst +++ b/doc/about.rst @@ -215,7 +215,7 @@ this way you can use the initial paper published in 2011 (see below). month = "08", doi = "10.3389/fninf.2011.00013", pubmed = "21897815", - url = "http://dx.doi.org/10.3389/fninf.2011.00013", + url = "https://doi.org/10.3389/fninf.2011.00013", issn = "1662-5196"} diff --git a/nipype/algorithms/confounds.py b/nipype/algorithms/confounds.py index 0349afdc23..a5feb89925 100644 --- a/nipype/algorithms/confounds.py +++ b/nipype/algorithms/confounds.py @@ -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 - `_. + `_. """ diff --git a/nipype/interfaces/ants/segmentation.py b/nipype/interfaces/ants/segmentation.py index 743f0a3903..d1531ac740 100644 --- a/nipype/interfaces/ants/segmentation.py +++ b/nipype/interfaces/ants/segmentation.py @@ -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.', diff --git a/nipype/interfaces/dipy/preprocess.py b/nipype/interfaces/dipy/preprocess.py index cc589f6579..285464847e 100644 --- a/nipype/interfaces/dipy/preprocess.py +++ b/nipype/interfaces/dipy/preprocess.py @@ -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 - `_, + `_, IEEE Transactions on Medical Imaging, 27(4):425-441, 2008. diff --git a/nipype/interfaces/dipy/simulate.py b/nipype/interfaces/dipy/simulate.py index 4a995c8fa9..b50b150f24 100644 --- a/nipype/interfaces/dipy/simulate.py +++ b/nipype/interfaces/dipy/simulate.py @@ -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 - `_. + `_. .. [Pierpaoli1996] Pierpaoli et al., Diffusion tensor MR imaging of the human brain, Radiology 201:637-648. 1996. """ diff --git a/nipype/interfaces/nipy/preprocess.py b/nipype/interfaces/nipy/preprocess.py index 252463e3f7..666aa27837 100644 --- a/nipype/interfaces/nipy/preprocess.py +++ b/nipype/interfaces/nipy/preprocess.py @@ -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 """ diff --git a/nipype/interfaces/petpvc.py b/nipype/interfaces/petpvc.py index 598dd898c5..c73b408bf3 100644 --- a/nipype/interfaces/petpvc.py +++ b/nipype/interfaces/petpvc.py @@ -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': diff --git a/nipype/workflows/dmri/fsl/artifacts.py b/nipype/workflows/dmri/fsl/artifacts.py index 3b29c5a07c..0bdd0a5d66 100644 --- a/nipype/workflows/dmri/fsl/artifacts.py +++ b/nipype/workflows/dmri/fsl/artifacts.py @@ -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 - `_, + `_, 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 - `_. + `_. Neuroimage. 21(88C):79-90. 2013. doi: 10.1016/j.neuroimage.2013.11.027 Example @@ -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 - `_, + `_, MRM 34(1):65-73. (1995). doi: 10.1002/mrm.1910340111. .. [Jenkinson03] Jenkinson M., `Fast, automated, N-dimensional - phase-unwrapping algorithm `_, + phase-unwrapping algorithm `_, MRM 49(1):193-197, 2003, doi: 10.1002/mrm.10354. """ @@ -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 `_. + tensor imaging `_. 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 @@ -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 `_. + MRI data `_. NeuroImage (2014). doi: 10.1016/j.neuroimage.2014.07.061