title: FATCAT: (an efficient) Functional and Tractographic Connectivity Analysis Toolbox.
abstract: We present a suite of software tools for facilitating the combination of functional magnetic resonance imaging (FMRI) and diffusion-based tractography from a network-focused point of view. The programs have been designed for investigating functionally derived gray matter networks and related structural white matter networks. The software comprises the Functional and Tractographic Connectivity Analysis Toolbox (FATCAT), now freely distributed with AFNI. This toolbox supports common file formats and has been designed to integrate as easily as possible with existing standard FMRI pipelines and diffusion software, such as AFNI, FSL, and TrackVis. The programs are efficient, run by commandline for facilitating group processing, and produce several visualizable outputs. Here, we present the programs and their underlying methods, and we also provide a test example of resting-state FMRI analysis combined with tractography. Tractography results are compared with existing methods, showing significantly reduced runtime and generally similar connectivity, but with important differences such as more circumscribed tract regions and more physiologically identifiable paths produced between several region-of-interest pairs. Currently, FATCAT uses only diffusion tensor-based tractography (one direction per voxel), but higher-order models will soon be included.
authors: 1 African Institute for Mathematical Sciences , Muizenberg, Western Cape, South Africa .
authors: Paul A
authors: PA
authors: Taylor
authors: Ziad S
authors: ZS
authors: Saad
mesh_terms: D001921:Brain / Q000033:anatomy & histology / Q000502:physiology; D001931:Brain Mapping / Q000379:methods*; D056324:Diffusion Tensor Imaging / Q000379:methods*; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008279:Magnetic Resonance Imaging / Q000379:methods; D009415:Nerve Net / Q000033:anatomy & histology / Q000502:physiology; D009434:Neural Pathways / Q000033:anatomy & histology / Q000502:physiology; D015203:Reproducibility of Results; D012146:Rest / Q000502:physiology; D012984:Software
references: Magn Reson Med. 2012 Oct;68(4):1097-108
references: 22246720
references: Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10422-7
references: 10468624
references: Neuroimage. 2006 Nov 1;33(2):531-41
references: 16938472
references: Neuroimage. 2003 Aug;19(4):1273-302
references: 12948688
references: Neuroimage. 2008 Jan 1;39(1):119-26
references: 17931889
references: Magn Reson Med. 2002 Oct;48(4):577-82
references: 12353272
references: Magn Reson Imaging. 2004 Feb;22(2):197-203
references: 15010111
references: Neuroimage. 2003 Jul;19(3):545-54
references: 12880786
references: Comput Biol Med. 2011 Dec;41(12):1142-55
references: 21975109
references: Magn Reson Med. 2011 Jul;66(1):154-67
references: 21695721
references: Neuroimage. 2006 Jul 1;31(3):1086-103
references: 16546404
references: Neuroimage. 2012 Jan 2;59(1):389-98
references: 21763773
references: Neuroimage. 2004 May;22(1):394-400
references: 15110032
references: Magn Reson Med. 2005 Dec;54(6):1377-86
references: 16247738
references: Magn Reson Med. 2005 May;53(5):1088-95
references: 15844157
references: J Neurosci Methods. 2008 Jul 15;172(1):137-41
references: 18501969
references: Neuroimage. 2007 Apr 1;35(2):488-500
references: 17254803
references: Neuroimage. 2012 Aug 15;62(2):768-73
references: 21945692
references: Proc Natl Acad Sci U S A. 1992 Jun 15;89(12):5675-9
references: 1608978
references: J Neurosci. 2007 Feb 28;27(9):2349-56
references: 17329432
references: Proc Natl Acad Sci U S A. 2010 Mar 9;107(10):4734-9
references: 20176931
references: Magn Reson Med. 2005 Nov;54(5):1194-206
references: 16161109
references: Biophys J. 1994 Jan;66(1):259-67
references: 8130344
references: Neuroimage. 2007 Oct 1;37(4):1267-77
references: 17706434
references: Magn Reson Imaging. 2003 Dec;21(10):1251-61
references: 14725933
references: Neuroimage. 1997 Oct;6(3):218-29
references: 9344826
references: Hum Brain Mapp. 2002 Jul;16(3):158-67
references: 12112769
references: Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):676-82
references: 11209064
references: Neuroimage. 2011 May 1;56(1):220-34
references: 21256221
references: Magn Reson Med. 2003 Nov;50(5):1077-88
references: 14587019
references: Magn Reson Med. 2004 Dec;52(6):1358-72
references: 15562495
references: J Neurosci. 2012 Feb 22;32(8):2773-82
references: 22357860
references: Neuroimage. 2007 Jan 1;34(1):144-55
references: 17070705
references: Proc Natl Acad Sci U S A. 2006 Sep 12;103(37):13848-53
references: 16945915
references: Brain Connect. 2011;1(3):169-83
references: 22433046
references: Magn Reson Med. 1995 Oct;34(4):537-41
references: 8524021
references: Neuroimage. 2012 Jun;61(2):324-41
references: 22120012
references: Comput Biomed Res. 1996 Jun;29(3):162-73
references: 8812068
references: NMR Biomed. 1995 Nov-Dec;8(7-8):375-86
references: 8739274
references: Front Syst Neurosci. 2012 Jan 18;5:104
references: 22279430
references: Brain. 2007 Mar;130(Pt 3):630-53
references: 17293361
references: Philos Trans R Soc Lond B Biol Sci. 2005 May 29;360(1457):1001-13
references: 16087444
references: Brain Dev. 2007 Mar;29(2):83-91
references: 16919409
references: Neuroimage. 2004;23 Suppl 1:S208-19
references: 15501092
references: Magn Reson Med. 2000 Oct;44(4):625-32
references: 11025519
references: Neuroimage. 1998 Feb;7(2):119-32
references: 9558644
references: Cereb Cortex. 2012 Feb;22(2):417-25
references: 21666131
references: Proc Natl Acad Sci U S A. 1990 Dec;87(24):9868-72
references: 2124706
references: Neuroimage. 2002 Sep;17(1):77-94
references: 12482069
references: Hum Brain Mapp. 1999;8(2-3):151-6
references: 10524607
references: Proc Natl Acad Sci U S A. 1998 Feb 3;95(3):803-10
references: 9448244
references: Magn Reson Med. 2003 Jan;49(1):7-12
references: 12509814
references: Hum Brain Mapp. 2008 Mar;29(3):346-62
references: 17455199
references: J Magn Reson. 2003 Mar;161(1):1-14
references: 12660106
references: J Magn Reson Imaging. 2003 Aug;18(2):242-54
references: 12884338
references: Ann Neurol. 1999 Feb;45(2):265-9
references: 9989633
references: Neuroimage. 2009 May 1;45(4):1199-211
references: 19162199
references: Neuroimage. 2008 May 1;40(4):1567-74
references: 18343159
references: PLoS One. 2012;7(9):e43415
references: 22970125
references: Magn Reson Med. 2008 Dec;60(6):1276-83
references: 19030160
references: Hum Brain Mapp. 2003 Apr;18(4):306-21
references: 12632468
references: NMR Biomed. 1995 Nov-Dec;8(7-8):333-44
references: 8739270