title: Fully automated rodent brain MR image processing pipeline on a Midas server: from acquired images to region-based statistics.
abstract: Magnetic resonance imaging (MRI) of rodent brains enables study of the development and the integrity of the brain under certain conditions (alcohol, drugs etc.). However, these images are difficult to analyze for biomedical researchers with limited image processing experience. In this paper we present an image processing pipeline running on a Midas server, a web-based data storage system. It is composed of the following steps: rigid registration, skull-stripping, average computation, average parcellation, parcellation propagation to individual subjects, and computation of region-based statistics on each image. The pipeline is easy to configure and requires very little image processing knowledge. We present results obtained by processing a data set using this pipeline and demonstrate how this pipeline can be used to find differences between populations.
authors: Neuro Image Research and Analysis Laboratories, Department of Psychiatry, University of North Carolina Chapel Hill, NC, USA.
authors: Francois
authors: F
authors: Budin
authors: Marion
authors: M
authors: Hoogstoel
authors: Patrick
authors: P
authors: Reynolds
authors: Michael
authors: M
authors: Grauer
authors: Shonagh K
authors: SK
authors: O'Leary-Moore
authors: Ipek
authors: I
authors: Oguz
keywords: automatic processing; magnetic resonance imaging; rodent; server
references: Proc SPIE Int Soc Opt Eng. 2011 Mar 15;7962:7962481-79624811
references: 21909228
references: Neuroimage. 2007 Sep 1;37(3):683-93
references: 17627846
references: Neuroimage. 2006 Feb 15;29(4):1058-65
references: 16213163
references: Neuroimage. 2009 Mar;45(1 Suppl):S133-42
references: 19059345
references: Neuroimage. 2010 Apr 1;50(2):416-27
references: 20035883
references: Brain Behav Immun. 2010 Jul;24(5):759-67
references: 19945527
references: Neuroimage. 2004;23 Suppl 1:S208-19
references: 15501092
references: IEEE Trans Med Imaging. 2010 Jun;29(6):1310-20
references: 20378467
references: Neuron. 2002 Jan 31;33(3):341-55
references: 11832223
references: IEEE Trans Med Imaging. 2007 Sep;26(9):1201-12
references: 17896593
references: Neuroimage. 2004;23 Suppl 1:S151-60
references: 15501084
references: Schizophr Res. 2009 Jul;112(1-3):46-53
references: 19487109
references: Neuroimage. 2008 Jan 1;39(1):32-9
references: 17942324
references: Proc SPIE Int Soc Opt Eng. 2011 Mar;7962:7962251-7962257
references: 21909227
references: Neuroimage. 2008 Aug 1;42(1):19-27
references: 18547819
references: Neuroimage. 2013 May 1;71:196-206
references: 23353030
references: Exp Neurol. 2005 Jan;191(1):77-85
references: 15589514
references: Magn Reson Med. 2007 Sep;58(3):454-62
references: 17763344
references: Proc SPIE Int Soc Opt Eng. 2009 Feb 1;7259:725943-725949
references: 20640188
references: Magn Reson Med. 1994 Feb;31(2):154-63
references: 8133751
references: Neuroimage. 2005 May 15;26(1):132-40
references: 15862213
references: Magn Reson Med. 2006 Aug;56(2):411-21
references: 16788917
references: Neuroimage. 2010 Aug 1;52(1):1-8
references: 20399275
references: Exp Neurol. 2006 Jun;199(2):408-15
references: 16483571
references: Korean J Radiol. 2007 May-Jun;8(3):185-91
references: 17554184
references: Cereb Cortex. 2005 May;15(5):639-45
references: 15342433
references: PLoS One. 2010 Sep 28;5(9):
references: 20927408
references: Neuroimage. 2005 Oct 15;28(1):165-74
references: 16023870
references: Int J Dev Neurosci. 2009 Oct;27(6):607-15
references: 19505567
references: J Comput Assist Tomogr. 1994 Mar-Apr;18(2):192-205
references: 8126267
references: Neuroscience. 2005;135(4):1203-15
references: 16165303
references: Med Image Anal. 2005 Oct;9(5):457-66
references: 16019252
references: J Magn Reson Imaging. 2008 Sep;28(3):574-87
references: 18777527
references: Neuroimage. 2011 Jun 1;56(3):1235-43
references: 21419226
references: Ann Neurol. 2008 Nov;64(5):535-46
references: 19067347
references: Magn Reson Med. 2006 Feb;55(2):439-49
references: 16402380
references: Neuroimage. 2006 Jan 1;29(1):99-105
references: 16084741
references: Magn Reson Med. 2004 Sep;52(3):559-65
references: 15334575
references: Med Image Anal. 2002 Jun;6(2):129-42
references: 12045000
references: AJNR Am J Neuroradiol. 2010 May;31(5):894-900
references: 20203117
references: Stroke. 2008 Aug;39(8):2348-53
references: 18535275
references: Med Image Anal. 2008 Feb;12(1):26-41
references: 17659998
references: Neuroimage. 2010 Feb 1;49(3):2366-74
references: 19837181
references: Cereb Cortex. 2007 Nov;17(11):2609-17
references: 17259644
references: Biol Psychiatry. 2010 May 1;67(9):846-54
references: 20044076
references: NMR Biomed. 2009 Aug;22(7):697-706
references: 19378292
references: Neuroimage. 2006 Sep;32(3):1016-23
references: 16806982
references: Cereb Cortex. 2010 Mar;20(3):534-48
references: 19520764
references: Neuroimage. 2006 Jul 1;31(3):1116-28
references: 16545965
references: Neuroimage. 2012 Nov 15;63(3):1633-45
references: 22836174
references: Magn Reson Med. 1996 Dec;36(6):893-906
references: 8946355