Skip to main content

Software for Neuroimaging Data Analysis

  • Living reference work entry
  • First Online:
  • 248 Accesses

Definition

Software is defined by as “a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.” We define Software for Neuroimaging Data Analysis as software whose primary goal is to support the extraction of information, and ultimately knowledge, from data acquired by an imaging device used on the brain (of human or animal subjects).

Detailed Description

Introduction

Tell us what you think about neuroimaging software, and we will tell you who you are. To some, using software to analyze data is little more than a technical step that stands between data acquisition and publishing. Doctoral students, postdocs, or technical assistants only need to operate the appropriate software, i.e., the script to run or the right sequence of buttons to press. To others, choosing, adapting, running, or developing the right software code is critical and requires investing significant time and resources.

Data analysis is one of the...

This is a preview of subscription content, log in via an institution.

References

  • Ad-Dab’bagh Y, Lyttelton O, Muehlboeck JS, Lepage C, Einarson D, Mok K, Ivanov O, Vincent RD, Lerch J, Fombonne E (2006) The CIVET image-processing environment: a fully automated comprehensive pipeline for anatomical neuroimaging research. In: Proceedings of the 12th annual meeting of the organization for human brain mapping, M. Corbetta, p S45

    Google Scholar 

  • Amazon. Amazon Elastic Compute Cloud (EC2) (n.d.) http://aws.amazon.com/ec2

  • Amazon. Amazon Web Service (AWS) (n.d.) http://aws.amazon.com/.

  • Ashburner J (2012) SPM: a history. Neuroimage 62(2):791–800. doi:10.1016/j.neuroimage.2011.10.025

    Article  PubMed  Google Scholar 

  • Avants BB, Yushkevich P, Pluta J, Minkoff D, Korczykowski M, Detre J, Gee JC (2010) The optimal template effect in hippocampus studies of diseased populations. Neuroimage 49(3):2457–2466. doi:10.1016/j.neuroimage.2009.09.062

    Article  PubMed Central  PubMed  Google Scholar 

  • Baggerly KA, Coombes KR (2009) Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology. Ann Appl Stat 3(4):1309–1334. doi:10.1214/09-AOAS291

    Article  Google Scholar 

  • Baillet S, Karl F, Robert O (2011) Academic software applications for electromagnetic brain mapping using MEG and EEG. Comput Intell Neurosci. doi:10.1155/2011/972050

    Google Scholar 

  • Begley CG, Ellis LM (2012) Drug development: raise standards for preclinical cancer research. Nature 483(7391):531–533

    Article  CAS  PubMed  Google Scholar 

  • Biswal BB, Mennes M, Zuo XN, Gohel S, Kelly C, Smith SM, Beckmann CF et al (2010) Toward discovery science of human brain function. Proc Natl Acad Sci 107(10):4734–4739. doi:10.1073/pnas.0911855107

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Di Martino A, Yan C-G, Li Q, Denio E, Castellanos FX, Alaerts K, Anderson JS et al (2013) The autism brain imaging data exchange: towards a large-scale evaluation of the intrinsic brain architecture in autism. Mol Psychiatry. doi:10.1038/mp.2013.78

    PubMed  Google Scholar 

  • Donoho DL (2010) An invitation to reproducible computational research. Biostatistics 11(3):385–388. doi:10.1093/biostatistics/kxq028

    Article  PubMed  Google Scholar 

  • Donoho DL, Maleki A, Rahman IU, Shahram M, Stodden V (2009) Reproducible research in computational harmonic analysis. Comput Sci Eng 11(1):8–18

    Article  Google Scholar 

  • Ed Gronenschild HBM, Habets P, Jacobs HIL, Mengelers R, Rozendaal N, van Os J, Marcelis M (2012) The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements. PLoS One 7(6):e38234. doi:10.1371/journal.pone.0038234

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Fischl B (2012) FreeSurfer. Neuroimage 62(2):774–781. doi:10.1016/j.neuroimage.2012.01.021

    Article  PubMed Central  PubMed  Google Scholar 

  • Goebel R (1996) BRAINVOYAGER: a program for analyzing and visualizing functional and structural magnetic resonance data sets. Neuroimage 3(3):S604. doi:10.1016/S1053-8119(96)80606-9

    Article  Google Scholar 

  • Halchenko YO, Hanke M (2012) Open is not enough. Let’s take the next step: an integrated, community-driven computing platform for neuroscience. Front Neuroinf 6:22. doi:10.3389/fninf.2012.00022

    Article  Google Scholar 

  • Hall D, Huerta MF, McAuliffe MJ, Farber GK (2012) Sharing heterogeneous data: the national database for autism research. Neuroinformatics 10(4):331–339

    Article  PubMed  Google Scholar 

  • Hanke M, Halchenko YO (2011) Neuroscience runs on GNU/Linux. Front Neuroinf 5:8. doi:10.3389/fninf.2011.00008

    Article  Google Scholar 

  • Ioannidis JP (2005) Why most published research findings are false. PLoS Med 2(8):e124. doi:10.1371/journal.pmed.0020124

    Article  PubMed Central  PubMed  Google Scholar 

  • Jenkinson M, Beckmann CF, Behrens TEF, Woolrich MW, Smith SM (2012) FSL. Neuroimage 62(2):782–790. doi:10.1016/j.neuroimage.2011.09.015

    Article  PubMed  Google Scholar 

  • Kennedy DN, Haselgrove C, Buccigrossi R, Grethe J (2009) Software development for neuroimaging: promoting community access and best practices through NITRC. In: Biomedical imaging: from nano to macro, 2009. ISBI’09. IEEE international symposium on, IEEE, pp 1146–1149. http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5193260

  • Klein A, Andersson J, Ardekani BA, Ashburner J, Avants B, Chiang MC, Christensen GE et al (2009) Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration. Neuroimage 46(3):786–802. doi:10.1016/j.neuroimage.2008.12.037

    Article  PubMed Central  PubMed  Google Scholar 

  • Luo XZJ, Kennedy DN (2009) Neuroimaging informatics tools and resources clearinghouse (NITRC) resource announcement. Neuroinformatics 7:55–56. doi:10.1385/NI

    Article  PubMed  Google Scholar 

  • Marcus DS, Olsen TR, Ramaratnam M, Buckner RL (2007) The extensible neuroimaging archive toolkit. Neuroinformatics 5(1):11–33

    PubMed  Google Scholar 

  • Mennes M, Biswal BB, Xavier Castellanos F, Milham MP (2013) Making data sharing work: the FCP/INDI experience. Neuroimage 82:683–691. doi:10.1016/j.neuroimage.2012.10.064

    Article  PubMed  Google Scholar 

  • MNI Software Tools (n.d.) http://www.bic.mni.mcgill.ca/ServicesSoftware/HomePage

  • Mueller SG, Weiner MW, Thal LJ, Petersen RC, Jack CR, Jagust W, Trojanowski JQ, Toga AW, Beckett L (2005) Ways toward an early diagnosis in Alzheimer’s disease: the Alzheimer’s disease neuroimaging initiative (ADNI). Alzheimer Dementia 1(1):55–66

    Article  Google Scholar 

  • Ou Y, Sotiras A, Paragios N, Davatzikos C (2011) DRAMMS: deformable registration via attribute matching and mutual-saliency weighting. Med Image Anal 15(4):622–639. doi:10.1016/j.media.2010.07.002

    Article  PubMed Central  PubMed  Google Scholar 

  • Poline J-B, Breeze JL, Ghosh S, Gorgolewski K, Halchenko YO, Hanke M, Haselgrove C et al (2012) Data sharing in neuroimaging research. Front Neuroinf 6:1–13. doi:10.3389/fninf.2012.00009

    Google Scholar 

  • Raymond E (1999) The cathedral and the bazaar. Knowl Technol Policy 12(3):23–49. doi:10.1007/s12130-999-1026-0

    Article  Google Scholar 

  • Simmons JP, Nelson LD, Simonsohn U (2011) False-positive psychology: undisclosed flexibility in data collection and analysis allows presenting anything as significant. Psychol Sci 22(11):1359–1366. doi:10.1177/0956797611417632

    Article  PubMed  Google Scholar 

  • The ADHD-200 Consortium (2012) The ADHD-200 consortium: a model to advance the translational potential of neuroimaging in clinical neuroscience. Front Syst Neurosci 6:62. doi:10.3389/fnsys.2012.00062

    PubMed Central  Google Scholar 

  • Toussaint N, Souplet JC, Fillard P (2007) MedINRIA: medical image navigation and research tool by INRIA. In: Proceedings of MICCAI, vol 7. http://med.inria.fr/

  • Woods RP, Cherry SR, Mazziotta JC (1992) Rapid automated algorithm for aligning and reslicing PET images. J Comput Assist Tomogr 16(4):620–633

    Article  CAS  PubMed  Google Scholar 

Further Reading

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jean Baptiste Poline .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media New York

About this entry

Cite this entry

Poline, J.B., Kennedy, D. (2014). Software for Neuroimaging Data Analysis. In: Jaeger, D., Jung, R. (eds) Encyclopedia of Computational Neuroscience. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7320-6_538-1

Download citation

  • DOI: https://doi.org/10.1007/978-1-4614-7320-6_538-1

  • Received:

  • Accepted:

  • Published:

  • Publisher Name: Springer, New York, NY

  • Online ISBN: 978-1-4614-7320-6

  • eBook Packages: Springer Reference Biomedicine and Life SciencesReference Module Biomedical and Life Sciences

Publish with us

Policies and ethics