title: Automatic analysis (aa): efficient neuroimaging workflows and parallel processing using Matlab and XML.
abstract: Recent years have seen neuroimaging data sets becoming richer, with larger cohorts of participants, a greater variety of acquisition techniques, and increasingly complex analyses. These advances have made data analysis pipelines complicated to set up and run (increasing the risk of human error) and time consuming to execute (restricting what analyses are attempted). Here we present an open-source framework, automatic analysis (aa), to address these concerns. Human efficiency is increased by making code modular and reusable, and managing its execution with a processing engine that tracks what has been completed and what needs to be (re)done. Analysis is accelerated by optional parallel processing of independent tasks on cluster or cloud computing resources. A pipeline comprises a series of modules that each perform a specific task. The processing engine keeps track of the data, calculating a map of upstream and downstream dependencies for each module. Existing modules are available for many analysis tasks, such as SPM-based fMRI preprocessing, individual and group level statistics, voxel-based morphometry, tractography, and multi-voxel pattern analyses (MVPA). However, aa also allows for full customization, and encourages efficient management of code: new modules may be written with only a small code overhead. aa has been used by more than 50 researchers in hundreds of neuroimaging studies comprising thousands of subjects. It has been found to be robust, fast, and efficient, for simple-single subject studies up to multimodal pipelines on hundreds of subjects. It is attractive to both novice and experienced users. aa can reduce the amount of time neuroimaging laboratories spend performing analyses and reduce errors, expanding the range of scientific questions it is practical to address.
authors: Brain and Mind Institute, Western University London, ON, Canada.
authors: Rhodri
authors: R
authors: Cusack
authors: Donders Institute for Brain, Cognition and Behaviour Nijmegen, Netherlands.
authors: Alejandro
authors: A
authors: Vicente-Grabovetsky
authors: MRC Cognition and Brain Sciences Unit Cambridge, UK.
authors: Daniel J
authors: DJ
authors: Mitchell
authors: Brain and Mind Institute, Western University London, ON, Canada.
authors: Conor J
authors: CJ
authors: Wild
authors: MRC Cognition and Brain Sciences Unit Cambridge, UK.
authors: Tibor
authors: T
authors: Auer
authors: Brain and Mind Institute, Western University London, ON, Canada.
authors: Annika C
authors: AC
authors: Linke
authors: Department of Otolaryngology, Washington University in St. Louis St. Louis, MO, USA.
authors: Jonathan E
authors: JE
authors: Peelle
keywords: diffusion tensor imaging (DTI); diffusion weighted imaging (DWI); functional magnetic resonance imaging (fMRI); multi-voxel pattern analysis (MVPA); neuroimaging; pipeline; software
references: Neuroimage. 2012 Apr 15;60(3):1759-70
references: 22209809
references: Neuroimage. 2012 Jul 16;61(4):1428-43
references: 22446492
references: Nat Rev Neurosci. 2006 Jul;7(7):523-34
references: 16791142
references: Trends Cogn Sci. 2006 Sep;10(9):424-30
references: 16899397
references: Front Neurosci. 2013 Dec 17;7:247
references: 24381539
references: Proc Natl Acad Sci U S A. 2010 Mar 9;107(10):4734-9
references: 20176931
references: Neuroimage. 2012 Feb 1;59(3):2142-54
references: 22019881
references: Front Neuroinform. 2013 Jul 08;7:12
references: 23847528
references: Alzheimers Dement. 2005 Jul;1(1):55-66
references: 17476317
references: Neuroimage. 2008 Jan 1;39(1):261-8
references: 17919925
references: Neuroimage. 2007 Oct 15;38(1):95-113
references: 17761438
references: Neuroimage. 2007 Jan 1;34(1):144-55
references: 17070705
references: IEEE Trans Med Imaging. 2008 Feb;27(2):161-70
references: 18334438
references: Neuroimage. 2006 Jul 15;31(4):1487-505
references: 16624579
references: Neuroimage. 1999 Jul;10(1):1-5
references: 10385576
references: Neuroimage. 2012 Oct 1;62(4):2222-31
references: 22366334
references: Philos Trans R Soc Lond B Biol Sci. 2001 Aug 29;356(1412):1323-39
references: 11545705
references: Neuroimage. 2009 Mar;45(1 Suppl):S163-72
references: 19059344
references: Magn Reson Imaging. 2009 Oct;27(8):1163-74
references: 19249168
references: Proc Natl Acad Sci U S A. 2006 Mar 7;103(10):3863-8
references: 16537458