Merge pull request #444 from MRtrix3/topup_ref

Add topup citation to revpe scripts

scripts/lib/citations.py

@@ -4,9 +4,10 @@
 
 list = [ ( 'ACT',           1,  'Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. Anatomically-constrained tractography: Improved diffusion MRI streamlines tractography through effective use of anatomical information. NeuroImage, 2012, 62, 1924-1938'),
          ( 'bet',           2, 'Smith, S. M. Fast robust automated brain extraction. Human Brain Mapping, 2002, 17, 143-155'),
-         ( 'eddy/topup',    2, 'Andersson, J. L. & Sotiropoulos, S. N. An integrated approach to correction for off-resonance effects and subject movement in diffusion MR imaging. NeuroImage, doi:10.1016/j.neuroimage.2015.10.019'),
+         ( 'eddy',          2, 'Andersson, J. L. & Sotiropoulos, S. N. An integrated approach to correction for off-resonance effects and subject movement in diffusion MR imaging. NeuroImage, 2016, 125, 1063-1078'),
          ( 'fast',          2, 'Zhang, Y.; Brady, M. & Smith, S. Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm. IEEE Transactions on Medical Imaging, 2001, 20, 45-57'),
          ( 'first',         2, 'Patenaude, B.; Smith, S. M.; Kennedy, D. N. & Jenkinson, M. A Bayesian model of shape and appearance for subcortical brain segmentation. NeuroImage, 2011, 56, 907-922'),
          ( 'FSL',           2, 'Smith, S. M.; Jenkinson, M.; Woolrich, M. W.; Beckmann, C. F.; Behrens, T. E.; Johansen-Berg, H.; Bannister, P. R.; De Luca, M.; Drobnjak, I.; Flitney, D. E.; Niazy, R. K.; Saunders, J.; Vickers, J.; Zhang, Y.; De Stefano, N.; Brady, J. M. & Matthews, P. M. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 2004, 23, S208-S219'),
          ( 'SIFT_followup', 1, 'Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. The effects of SIFT on the reproducibility and biological accuracy of the structural connectome. NeuroImage, 2015, 104, 253-265'),
-         ( 'Skare2010',     2, 'Skare, S. & Bammer, R. Jacobian weighting of distortion corrected EPI data. Proceedings of the International Society for Magnetic Resonance in Medicine, 2010, 5063') ]
+         ( 'Skare2010',     2, 'Skare, S. & Bammer, R. Jacobian weighting of distortion corrected EPI data. Proceedings of the International Society for Magnetic Resonance in Medicine, 2010, 5063'),
+         ( 'topup',         2, 'Andersson, J.L.R.; Skare, S. & Ashburner, J. How to correct susceptibility distortions in spin-echo echo-planar images: application to diffusion tensor imaging. NeuroImage, 2003, 20, 870-888') ]

scripts/revpe_distcorr

@@ -27,7 +27,7 @@ from lib.runCommand    import runCommand
 from lib.warnMessage   import warnMessage
 
 lib.app.author = 'Robert E. Smith ([email protected])'
-lib.app.initCitations([ 'eddy/topup', 'FSL' ])
+lib.app.initCitations([ 'eddy', 'FSL', 'topup' ])
 lib.app.initParser('Perform EPI distortion correction of a volume series using a reversed phase-encode image pair to estimate the inhomogeneity field')
 lib.app.parser.add_argument('pe_axis',   help='The phase encode direction / axis; can be an axis number (0, 1 or 2) or a code (e.g. AP, LR, IS)')
 lib.app.parser.add_argument('image1of2', help='The first image of the reversed-PE image pair')

scripts/revpe_dwicombine

@@ -33,7 +33,7 @@ from lib.runCommand    import runCommand
 from lib.warnMessage   import warnMessage
 
 lib.app.author = 'Robert E. Smith ([email protected])'
-lib.app.initCitations([ 'eddy/topup', 'FSL', 'Skare2010' ])
+lib.app.initCitations([ 'eddy', 'FSL', 'Skare2010', 'topup' ])
 lib.app.initParser('Perform EPI distortion & recombination of a pair of image volumes, where the diffusion gradient table is identical between the two series, but the phase-encode direction is reversed')
 lib.app.parser.add_argument('pe_axis', help='The phase encode direction / axis; can be an axis number (0, 1 or 2) or a code (e.g. AP, LR, IS)')
 lib.app.parser.add_argument('series1', help='The first input image series')