From 299971a38d3885b5f7f63967ad3952648bad5b8e Mon Sep 17 00:00:00 2001 From: Robert Smith Date: Fri, 12 Feb 2016 23:35:15 +1100 Subject: [PATCH] Add topup citation to revpe scripts --- scripts/lib/citations.py | 5 +++-- scripts/revpe_distcorr | 2 +- scripts/revpe_dwicombine | 2 +- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/scripts/lib/citations.py b/scripts/lib/citations.py index 042ecc2ade..f7b3812e3a 100644 --- a/scripts/lib/citations.py +++ b/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') ] diff --git a/scripts/revpe_distcorr b/scripts/revpe_distcorr index d56adcb290..71803bc12a 100755 --- a/scripts/revpe_distcorr +++ b/scripts/revpe_distcorr @@ -27,7 +27,7 @@ from lib.runCommand import runCommand from lib.warnMessage import warnMessage lib.app.author = 'Robert E. Smith (robert.smith@florey.edu.au)' -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') diff --git a/scripts/revpe_dwicombine b/scripts/revpe_dwicombine index 4477716a78..51f8f04da9 100755 --- a/scripts/revpe_dwicombine +++ b/scripts/revpe_dwicombine @@ -33,7 +33,7 @@ from lib.runCommand import runCommand from lib.warnMessage import warnMessage lib.app.author = 'Robert E. Smith (robert.smith@florey.edu.au)' -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')