---
abstract: 'Neuroimaging in vivo is becoming popular from the last two decades. The primary quest of neuroimaging is to better-understanding the functions of various brain areas pertaining to various cognitive processes of interest. Though there are several neuroimaging techniques available currently, the functional Magnetic Resonance Imaging (fMRI) is playing an important role in the field of Imaging Neuroscience. In this paper an introduction to fMRI, the issues related to experimental design and analysis will be presented. This paper also discusses some of the neuroinformatics tools available for fMRI research. '
altloc: []
chapter: ~
commentary: ~
commref: ~
confdates: ~
conference: ~
confloc: ~
contact_email: ~
creators_id: []
creators_name:
- family: Miyapuram
given: Krishna P.
honourific: ''
lineage: ''
- family: Pammi
given: V. S. Chandrasekhar
honourific: ''
lineage: ''
- family: Ahmed
given: Ahmed
honourific: ''
lineage: ''
- family: Bapi
given: Raju S.
honourific: ''
lineage: ''
date: 2007-04
date_type: published
datestamp: 2007-04-26
department: ~
dir: disk0/00/00/54/85
edit_lock_since: ~
edit_lock_until: ~
edit_lock_user: ~
editors_id: []
editors_name: []
eprint_status: archive
eprintid: 5485
fileinfo: /style/images/fileicons/text_html.png;/5485/1/NeuroInformatics.html
full_text_status: public
importid: ~
institution: ~
isbn: ~
ispublished: unpub
issn: ~
item_issues_comment: []
item_issues_count: 0
item_issues_description: []
item_issues_id: []
item_issues_reported_by: []
item_issues_resolved_by: []
item_issues_status: []
item_issues_timestamp: []
item_issues_type: []
keywords: 'fMRI, Experimental design, Statistical Parametric Mapping'
lastmod: 2011-03-11 08:56:49
latitude: ~
longitude: ~
metadata_visibility: show
note: ~
number: ~
pagerange: ~
pubdom: FALSE
publication: ~
publisher: ~
refereed: FALSE
referencetext: |
Biswal, B.B., Ulmer, J.L., 1999. Blind source separation of multiple signal sources of fMRI data sets using independent component analysis. J. Comput. Assist. Tomogr. 23, 265– 271.
Chein, J. M. and Schneider, W. (2003). Designing effective fMRI experiments. In Grafman, J. and Robertson, I., editors, Handbook of Neuropsychology. Elsevier Science B.V., Amsterdam.
Cohen, M. S. and Bookheimer, S. Y. (1994). Functional magnetic resonance imaging. Trends in Neurosciences, 17:268–277.
Cox, R. W. (1996) AFNI – Software for Analysis and Visualization of Functional Magnetic Resonance Neuroimages. Computers and Biomedical Research 29:162-173.
Culham, J. C. (2005). Functional neuroimaging: Experimental design and analysis. In Cabeza, R. and Kingstone, A., editors, Handbook of Functional Neuroimaging of Cognition, 2nd edition. MIT Press, Cambridge MA.
Davatzikos C., Ruparel K., Fan Y., Shen D. G., Acharyya M., Loughead J. W., Gur R. C., and Langleben D. D. (2005). Classifying spatial patterns of brain activity with machine learning methods: application to lie detection. NeuroImage, 28:663–668.
Friston, K. J. (1997). Imaging cognitive anatomy. Trends in Cognitive Sciences, 1:21–27.
Friston, K. (1998). Imaging neuroscience: principles or maps? Proc. Natl. Acad. Sci. USA, 95:796–802.
Friston K.J., Glaser D.E., Henson R.N.A., Kiebel S., Phillips C., and Ashburner J. (2002). Classical and Bayesian Inference in Neuroimaging: Applications. NeuroImage, 16:484-512.
Friston, K. J., Harrison, L., and Penny, W. (2003). Dynamic causal modelling. NeuroImage, 19:1273–1302.
Friston, K. , Ashburner, J., Kiebel, S., Nichols, T., and Penny, W., Eds, (2006) Statistical Parametric Mapping: The analysis of functional brain images. Elsevier, London.
Haynes, J-D., and Rees G. (2006). Decoding mental states from brain activity in humans. Nature Reviews Neuroscience 7: 523–534.
Heeger, D. J. and Ress, D. (2002). What does fMRI tell us about neural activity? Nature Reviews, 3:142–150.
Hornak, J. P. (2002). The basics of MRI. Online book at: http://www.cis.rit.edu/htbooks/mri/, Rochester, NY.
Makeig, S., Jung, T.P., Bell, A.J., Ghahremani, D., Sejnowski, T.J., 1997. Blind separation of auditory event-related brain responses into independent components. Proc. Natl. Acad. Sci. U. S. A. 94, 10979–10984.
McKeown, M.J., Jung, T.P., Makeig, S., Brown, G., Kindermann, S.S., Lee, T.W., Sejnowski, T.J., 1998. Spatially independent activity patterns in functional MRI data during the stroop color-naming task. Proc. Natl. Acad. Sci. U. S. A. 95, 803–810.
Mechelli, A., Henson, R. N. A., Price, C. J., and Friston, K. J. (2003). Comparing event-related and epoch analysis in blocked design fMRI. NeuroImage, 18:806–810.
Mitchell, T., Hutchinson, R., Niculescu, R., Pereira, F., Wang, X., Just M., and Newman, S. (2004). Learning to decode cognitive states from brain images. Machine Learning, 57:145–175.
Ogawa, S., Lee, T. M., Kay, A. R., and Tank, D. W. (1990). Brain magnetic resonance imaging with contrast dependent on blood oxygenation. Proceedings of the National Academy of Sciences, USA, 87:9868–9872.
Ogawa, S., Tank, D. W., Menon, R., Ellermann, J. M., Kim, S., Merkle, H., and Ugurbil, K. (1992). Intrinsic signal changes accompanying sensory stimulation: Functional brain mapping with magnetic resonance imaging. Proceedings of the National Academy of Sciences, USA, 89:5951–5955.
Partain, C. L. (2006). JMRI special issue: Clinical potential of brain mapping using MRI, Journal of Magnetic Resonance Imaging, 23:785–786
Smith, S.M., Jenkinson, M., Woolrich, M.W., Beckmann, C.F., Behrens, T.E.J., Johansen-Berg, H., Bannister, P.R., De Luca, M., Drobnjak, I., Flitney, D.E., Niazy, R., Saunders, J., Vickers, J., Zhang, Y., De Stefano, N., Brady, J.M., and Matthews, P.M. (2004). Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-219
Talairach P, Tournoux J. (1988). A Stereotactic Coplanar Atlas of the Human Brain. Stuttgart: Thieme
Ugurbil, K., Toth, L., and Kim, D. S. (2003). How accurate is magnetic resonance imaging of brain function? Trends in Neuroscience, 26:108–114.
Volkow, N. D., Rosen, B., and Farde, L. (1997). Imaging the living human brain: Magnetic resonance imaging and positron emission tomography. Proceedings of National Academy of Sciences, USA, 94:2787–2788.
relation_type: []
relation_uri: []
reportno: ~
rev_number: 8
series: ~
source: ~
status_changed: 2007-09-12 17:10:20
subjects:
- brain-img
succeeds: ~
suggestions: ~
sword_depositor: ~
sword_slug: ~
thesistype: ~
title: 'Neuroinformatics Tools for Functional MRI: Experimental Design and Data Analysis'
type: other
userid: 6034
volume: ~