fMRI Links

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Connect

Papers

New

Brain

June 2011

Localizers

May 2011

Controversy

Blogs

Misc

DTI

April 24, 2011

MRI artifacts / simulation

New

Groups

de Bruijn

Papers

Tools

Topics

MATLAB code

  • How to transform an ROI image into a range of coordinates?
     
    Nii = nifti('ROI.img');
    X = Nii.dat(:,:,:);
    ind = find(X(:));
    dm = size(X);
    i = rem(ind-1,dm(1))+1;
    j = rem(floor((ind-1)/dm(1)),dm(2))+1;
    k = floor((ind-1)/(dm(1)*dm(2)))+1;
    [i j k]
    The i, j and k indices can then be converted to mm coordinates by:
    xyz = (Nii.mat(1:3,:)*[i j k ones(size(i))]')'
     

Groups

March 2011

  • Durston et al. (2009), Neurosci Biobehav Rev 33(5):674-89
     
  • Varela et al. (2007), Biol Psychiatry 61(12):1361-1369 
     
  • Shaw et al. (2006) Arch Gen Psychiatry 63(5):540-9 
     
  • Mackie et al. (2007), Am J Psychiatry 164(4):647-55 
     
  • Automatic segmentation of the ventricular system from MR images of the human brain 
    Schnack HG, Hulshoff Pol HE, Baaré WFC, Viergever MA, Kahn RS 
    NeuroImage. 2001; 14: 95-104.
     
  • Automated separation of gray and white matter from MR images of the human brain 
    Schnack HG, Hulshoff Pol HE, Baaré WFC, Staal WG, Viergever MA, Kahn RS. 
    Neuroimage. 2001; 13:230-237 
     
  • Centenary of Brodmann’s map – conception and fate
    Zilles K, Amunts K (2010) 
    Nature Reviews Neuroscience 2010 Jan .
     
  • Cytoarchitecture of the cerebral cortex – more than localization 
    Amunts K, Schleicher A, Zilles K (2007)
    Neuroimage 37: 1061-1065
     
  • Quantitative analysis of cyto- and receptor architecture of the human brain
    Zilles K, Schleicher A, Palomero-Gallagher N, Amunts K (2002) 
    In: /Brain Mapping: The Methods/, J. C. Mazziotta and A. Toga (eds.), USA: Elsevier, 2002, p. 573-602.
      
  • Sylvian fissure size in schizophrenia measured with the magnetic resonance imaging rating protocol of the Consortium to Establish a Registry for Alzheimer's Disease
    JM Schwartz, E Aylward, PE Barta, LE Tune and GD Pearlson
    Am J Psychiatry 1992;  149:1195-1198 
     
  • Multi-level bootstrap analysis of stable clusters in resting-state fMRI
    Pierre Bellec, Pedro Rosa-Neto, Oliver C. Lyttelton, Habib Benali, and Alan C. Evans
    NeuroImage, Volume 51, Issue 3, 1 July 2010, Pages 1126-1139 
    http://dx.doi.org/10.1016/j.neuroimage.2010.02.082 
     
  • A nonlinear identification method to study effective connectivity in functional MRI 
    X. Li; G. Marrelec; R.F. Hess; H. Benali 
    Medical Image Analysis, 2010, 14(1):30-38
     
  • An enhanced voxel-based morphometry method to investigate structural changes: application to Alzheimer's disease 
    X. Li;A. Messé;G. Marrelec;M. Pélégrini-Issac;H. Benali
    Neuroradiology, 2010, 52(3):203-13  
     
  • Mapping Cognitive Processes onto the Brain: Mind the Gap
    Diane F. Halpern
    Brain and Cognition, Volume 42, Issue 1, February 2000, Pages 128-130
     
  • Brain plasticity related to the consolidation of motor sequence learning and motor adaptation
    K. Debas;J. Carrier;P. Orban;M. Barakat;O. Lungu;G. Vandewalle;A. Hadj Tahar;P. Bellec;A. Karni;L.G. Ungerleider;H. Benali;J. Doyon
    Proceedings of the National Academy of Sciences of the USA, 2010, 107(41):17839-17844
     
  • Abnormal Brain Default-Mode Network Functional Connectivity in Drug Addicts
    by Ning Ma, Ying Liu, Xian-Ming Fu, et al.
    PLoS ONE, Vol. 6, No. 1. (26 January 2011), e16560.
    http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016560 
     
  • The quantitative evaluation of functional neuroimaging experiments: the NPAIRS data analysis framework.
    Strother SC, Anderson J, Hansen LK, Kjems U, Kustra R, Sidtis J, Frutiger S, Muley S, LaConte S, Rottenberg D.
    Neuroimage. 2002 Apr;15(4):747-71.
     
  • The cortical topography of human anorectal musculature
    Turnbull GK, Hamdy S, Aziz Q, Singh KD, and Thompson DG 
    Gastroenterology 117: 32-39, 1999
     
  • Enhancing effects of flavored nutritive stimuli on cortical swallowing network activity 
    Arash Babaei1, Mark Kern1, Stephen Antonik1, Rachel Mepani1, B. Douglas Ward2, Shi-Jiang Li2, James Hyde2, and Reza Shaker 
    Published online before print May 2010, doi: 10.?1152/?ajpgi.?00161.?2010
    AJP - GI August 2010 vol. 299 no. 2 G422-G429
     
  • Cerebral cortical representation of reflexive and volitional swallowing in humans 
    Kern MK, Jaradeh S, Arndorfer RC, and Shaker R. 
    Am J Physiol Gastrointest Liver Physiol 280: G354-G360, 2001
     
  • Cerebral cortical representation of external anal sphincter contraction: effect of effort
    Mark K. Kern, Ronald C. Arndorfer, James S. Hyde, and Reza Shaker
    September 2003, doi: 10.?1152/?ajpgi.?00201.?2003 
    AJP - GI February 2004 vol. 286 no. 2 G304-G311
     

February 2011

Jan 2011

  • The Neural Basis of Intuitive Best Next-Move Generation in Board Game Experts
    Xiaohong Wan, Hironori Nakatani, Kenichi Ueno, Takeshi Asamizuya, Kang Cheng, and Keiji Tanaka
    Science 21 January 2011: 341-346. [DOI:10.1126/science.1194732] 
     

Dec 2010

  •  Resting-State fMRI Data Analysis Toolkit (REST) 
    http://restfmri.net
     
  • Two distinct neural effects of blinking on human visual processing
    Davina Bristow, Chris Frith, Geraint Rees
    NeuroImage, Volume 27, Issue 1, 1 August 2005, Pages 136-145
     
  • SurfStat - A Matlab toolbox for the statistical analysis of univariate and multivariate surface and volumetric data using linear mixed effects models and random field theory
    Keith J. Worsley
    http://www.math.mcgill.ca/keith/surfstat/
     
  • Nathan Kline Institute (NKI) / Rockland Sample
    http://fcon_1000.projects.nitrc.org/indi/pro/nki.html  
     

New

Methodology

  • Ambiguous Results in Functional Neuroimaging Data Analysis Due to Covariate Correlation
    Andrade et al.
    NeuroImage 10, 483–486 (1999)
     
  • Effects on Simultaneous Tests of Beta_k
    Section 7.6 ("Multicollinearity and its effects") 
    Neter, Kutner, Nachtsheim, and Wasserman 
    Applied Linear Statistical Models, 4th ed.
     

Music

  • Music training leads to the development of timbre-specific gamma band activity
    Antoine J. Shahin, Larry E. Roberts, Wilkin Chau, Laurel J. Trainor, Lee M. Miller
    NeuroImage, Volume 41, Issue 1, 15 May 2008, Pages 113-122
     
  • Investigating brain response to music: A comparison of different fMRI acquisition schemes
    Karsten Mueller, Toralf Mildner, Thomas Fritz, Jöran Lepsien, Christian Schwarzbauer, Matthias L. Schroeter, Harald E. Möller
    NeuroImage, In Press, Corrected Proof, Available online 20 August 2010
     
  • Brain changes after learning to read and play music 
    Lauren Stewart, Rik Henson, Knut Kampe, Vincent Walsh, Robert Turner, Uta Frith
    NeuroImage, Volume 20, Issue 1, September 2003, Pages 71-83
     
  • Scanning silence: Mental imagery of complex sounds  
    Nico Bunzeck, Torsten Wuestenberg, Kai Lutz, Hans-Jochen Heinze, Lutz Jancke
    NeuroImage, Volume 26, Issue 4, 15 July 2005, Pages 1119-1127
     

New

  • Presentation Help : Help Guide : Stimuli : Auditory Stimuli
    http://www.neurobs.com/presentation/docs 
     
  • SPM Course 2011
    February 16–18, 2011 - Zurich
    http://www.socialbehavior.uzh.ch/symposiaandworkshops/spm2011.html
     
  • Matt Roser - Autism study (Department of Psychology, University of Plymouth UK)
    http://www.psy.plymouth.ac.uk/research/mattroser/autism_study.html
     
  • Human Brain Mapping, Special Issue: Meta-Analysis of Functional Brain Mapping
    Volume 25 Issue 1 , Pages 1 - 198 (May 2005)
    http://www3.interscience.wiley.com/journal/110474166/issue?CRETRY=1&SRETRY=0 
     
  • NeuroImaging Data Access Group (NIDAG)
    http://www.nidag.org 
     
  • An amygdala response to fearful faces with covered eyes 
    Aziz U.R. Asghar, Yi-Chieh Chiu, Glyn Hallam, Siwei Liu, Hannah Mole, Hayley Wright and Andrew W. Young
    Neuropsychologia, Volume 46, Issue 9, July 2008, Pages 2364-2370
    http://dx.doi.org/10.1016/j.neuropsychologia.2008.03.015 
     
  • Amygdala
    http://en.wikipedia.org/wiki/Amygdala
     
  • Applications of real-time fMRI
    R. Christopher deCharms
    Nature Reviews Neuroscience 9, September 2008, pp. 720-729
    doi:10.1038/nrn2414
     
  • Neurobehavioral Systems / Presentation
    http://www.neurobs.com/presentation/
     
  • fMRI - MATLAB 
    oc = spm_get_orgi_coord([-13 32 25],'0001_seg_sn.mat','wr0001.nii')
     
  • Subject: Re: Multiple regression: testing an interaction at the second level
    From: Thomas Nichols
    https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=SPM;PPOtEw;20080318094435%2B0000 
     
  • http://www.fz-juelich.de/inm/inm-1/spm_anatomy_toolbox
     
  • High resolution fMRI of subcortical regions during visual erotic stimulation at 7 T
    Martin Walter, Joerg Stadler, Claus Tempelmann, Oliver Speck and Georg Northoff
    Magnetic Resonance Materials in Physics, Biology and Medicine, Volume 21, Numbers 1-2 / March, 2008, pp. 103-111
    http://www.springerlink.com/content/0245v48150m48423/
     
  • The human hippocampus at 7 T - In vivo MRI
    Jens M. Theysohn, O. Kraff, S. Maderwald, M.U. Schlamann, A. de Greiff, M. Forsting, S.C. Ladd, M.E. Ladd, E.R. Gizewski
    Hippocampus, Volume 19 Issue 1, Pages 1-7, Aug 2008
    Theysohn-FMRI-7T.2008.pdf
     
  • Multivariate models of inter-subject anatomical variability.
    Ashburner J, Klöppel S.
    Neuroimage. 2010 Mar 27. [Epub ahead of print]
    http://dx.doi.org/10.1016/j.neuroimage.2010.03.059
     
  • Age- and Sex-related effects on the neuroanatomy of healthy elderly 
    Lemaître H, Crivello F, Grassiot B, Alpérovitch A, Tzourio C, Mazoyer BM.
    NeuroImage 2005, 26:900-911.
    http://www.cyceron.fr/upload/editeur/Lemaitre_H_2005.pdf 
     
  • Kyo's Lab
    http://www.nemotos.net/?p=200
     
  • Development of Korean standard brain templates 
    http://jkms.org/Synapse/Data/PDFData/0063JKMS/jkms-20-483.pdf 
     
  • What we can do and what we cannot do with fMRI
    Nikos K. Logothetis 
    Nature 453, 869-878 (12 June 2008) doi:10.1038/nature06976
     
  • Neuroscientist: my data published without authorization are 'misleading'
    Alison Abbott 
    Nature 454, 6-7 (2 July 2008) doi:10.1038/454006a
     
  • Voxel-Based Study of Structural Changes in First-Episode Patients with Bipolar Disorder
    Caleb M. Adler, Melissa P. DelBello, Kelly Jarvis, Ari Levine, John Adams, Stephen M. Strakowski
    Biological Psychiatry, Volume 61, Issue 6, 15 March 2007, Pages 776-781
    ADLER-VBM.2007.pdf
     
  • Changes in Gray Matter Volume in Patients with Bipolar Disorder
    Caleb M. Adler, Ari D. Levine, Melissa P. DelBello, Stephen M. Strakowski
    Biological Psychiatry, Volume 58, Issue 2, 15 July 2005, Pages 151-157
    ADLER-VBM.2005.pdf
     
  • Individual voxel-based analysis of gray matter in focal cortical dysplasia
    O. Colliot, N. Bernasconi, N. Khalili, S.B. Antel, V. Naessens, A. Bernasconi
    NeuroImage, Volume 29, Issue 1, 1 January 2006, Pages 162-171
    COLLIOT-VBM.2006.pdf
     
  • Hypothalamic gray matter changes in narcoleptic patients
    B. Draganski, P. Geisler, G. Hajak, G. Schuierer, U. Bogdahn, J. Winkler, A. May 
    Nature Medicine 8, 1186-1188 (31 October 2002) doi:10.1038/nm1102-1186 Letters to Editor
     
  • Reduced cortical gray matter in narcolepsy: Preliminary findings with voxel-based morphometry
    Christian Kaufmann, Andreas Schuld, Thomas Pollmächer, and Dorothee P. Auer
    Neurology, Jun 2002; 58: 1852 - 1855.
     
  • Detection of grey matter loss in mild Alzheimer's disease with voxel based morphometry
    G B Frisoni, C Testa, A Zorzan, F Sabattoli, A Beltramello, H Soininen, and M P Laakso
    J. Neurol. Neurosurg. Psychiatry, December 1, 2002; 73(6): 657 - 664.
     
  • Cephos Corp.
    http://www.cephoscorp.com  
     
  • No Lie MRI Inc.
    http://www.noliemri.com/products/Overview.htm
     
  • Confirming white matter fMRI activation in the corpus callosum: co-localization with DTI tractography
    Mazerolle EL, Beyea SD, Gawryluk JR, Brewer KD, Bowen CV, D'Arcy RC.
    Neuroimage. 2010 Apr 1;50(2):616-21. Epub 2010 Jan 4.
     
  • Optimizing the detection of white matter fMRI using asymmetric spin echo spiral.
    Gawryluk JR, Brewer KD, Beyea SD, D'Arcy RC
    Neuroimage. 2009 Mar 1;45(1):83-8. Epub 2008 Nov 21.
     
  • BOLD correlates of trial-by-trial reaction time variability in gray and white matter: a multi-study fMRI analysis.
    Yarkoni T, Barch DM, Gray JR, Conturo TE, Braver TS.
    PLoS One. 2009;4(1):e4257. Epub 2009 Jan 23.
     
  • Interhemispheric transmission of visuomotor information in humans: fMRI evidence.
    Tettamanti M, Paulesu E, Scifo P, Maravita A, Fazio F, Perani D, Marzi CA
    J Neurophysiol. 2002 Aug;88(2):1051-8.
     
  • Estimating sample size in functional MRI (fMRI) neuroimaging studies: statistical power analyses.
    J. E. Desmond, G. H. Glover
    J Neurosci Methods, Vol. 118, No. 2. (30 August 2002), pp. 115-128
    http://www.citeulike.org/user/svbcrypto/article/890123 
     
  • Power calculation for group fMRI studies accounting for arbitrary design and temporal autocorrelation
    Jeanette A. Mumford and Thomas E. Nichols
    NeuroImage, Volume 39, Issue 1, 1 January 2008, Pages 261-268
    doi:10.1016/j.neuroimage.2007.07.061 
     
  • http://www.cogsci.ed.ac.uk/~jneumann/HBM2005/hbm2005_poster.pdf
     
  • Zhang & Sejnowski (2000) PNAS 97, 5621-5626
     
  • Kiselev et al (2004)
    NeuroImage 20, 1765-1774
    http://www.cogsci.ed.ac.uk/~jneumann/HBM2005/hbm2005_poster.pdf
     
  • Title
    https://vuiis.vanderbilt.edu/Publications/VUIIS_Retreat_2005/Saikat_Poster.pdf
     
  • Structural Equation Modelling (SEM) for fMRI using Matlab
    http://www.abdn.ac.uk/~men204/SEM.htm
    The method of image analysis described by Dr Meyer-Lyndenberg (Stein et al, 2007, NeuroImage, 36, 736-45) was developed using the above code as a starting point.
     
  • Detecting and Adjusting for Artifacts in fMRI Time Series Data
    http://www.bangor.ac.uk/~pss412/imaging/robustWLS.html
       
  • Generalized mutual information fMRI analysis: a study of the Tsallis q parameter
    Physica A: Statistical Mechanics and its Applications
    Volume 344, Issues 3-4, 15 December 2004, Pages 705-711
     
  • Shannon entropy applied to the analysis of event-related fMRI time series
    NeuroImage, Volume 20, Issue 1, September 2003, Pages 311-317
     
  • P1-274: Diminished FMRI word repetition effects in mild Alzheimer's disease
    Alzheimer's and Dementia, Volume 4, Issue 4, Supplement 1, July 2008, Page T297
    John M. Olichney, Andrew Stringfellow, Jason R. Taylor, Shiao-Hui Chan, Dieter Hillert, David Salmon, Vicente Iragui-Madoz, Marta Kutas
     
  • Resampling fMRI time series
    Ola Friman, and Carl-Fredrik Westin
    NeuroImage, Volume 25, Issue 3, 15 April 2005, Pages 859-867
     
  • Computing Brain Activity Maps from fMRI Time-Series Images
    Gordon E. Sarty
    ISBN-13: 9780511258381
     
  • Decomposing Components of Task Preparation with Functional Magnetic Resonance Imaging.
    M. Brass and D.Y. von Cramon (2004)
    Journal of Cognitive Neuroscience, 16(4):609-620.
     
  • Internally generated and directly cued task sets: an investigation with fMRI.
    Forstmann BU, Brass M, Koch I, von Cramon DY.
    Neuropsychologia. 2005;43(6):943-52
    http://www.ncbi.nlm.nih.gov/pubmed/15716164
     
  • Using Replicator Dynamics for Analyzing fMRI Data of the Human Brain
    G. Lohmann and S. Bohn (2002)
    IEEE Transactions on Medical Imaging, 21(5):485-492.
    http://ieeexplore.ieee.org/iel5/42/21763/01009384.pdf?arnumber=1009384
     
  • Detecting and adjusting for artifacts in fMRI time series data
    Jorn Diedrichsen and Reza Shadmehr
    Neuroimage, 27(3), 624-634, 2005
    http://www.bangor.ac.uk/~pss412/pubs/Neuroimage_2005.pdf
     
  • Canonical Correlation Analysis: An Overview with Application to Learning Methods
    Hardoon et al.
    Neural Computation 2004; 16: 2639-2664
     
  • Movement-related effect in fMRI time-series
    Friston KJ, Williams SR, Howard R Frackowiak RSJ and Turner R (1995)
    Mag. Res. Med. 35:346-355
     
  • Improved Image Registration by Using Fourier Interpolation
    W. F. Eddy, M. Fitzgerald and D. C. Noll (1996)
    Mag. Res. Med. 36(6):923-931
     
  • Real-Time 3D Image Registration for Functional MRI
    R. W. Cox and A. Jesmanowicz (1999)
    Submitted to MRM (April 1999)
    http://varda.biophysics.mcw.edu/~cox/index.html
     
  • fMRI RFX 
    http://rfxplot.sourceforge.net/features/features.html
     
  • ARCTIC (Automatic Regional Cortical ThICkness)
    Voxel-based cortical thickness toolbox
    http://www.nitrc.org/frs/?group_id=186
     
  • Neuromorphometrics Inc.
    http://neuromorphometrics.com
     
  • Ambiguous Results in Functional Neuroimaging Data Analysis Due to Covariate Correlation
    Andrade et al. 
    Neuroimage 1999 10, 483–486.
     
  • PSM post ... Total Intracranial Volume Many people simply add GM+WM+CSF, but John has repeatedly warned that this needs very careful checking due to inconsistencies in the estimation of cisternal CSF
     
  • Keihaninejad S et al.
     
  • A robust method to estimate the intracranial volume across MRI field strengths (1.5T and 3T)
    Shiva Keihaninejada, Rolf A. Heckemanna, b, Gianlorenzo Fagioloc, Mark R. Symmsd, Joseph V. Hajnalc, Alexander Hammers and The Alzheimer's Disease Neuroimaging Initiative
    NeuroImage, Volume 50, Issue 4, 1 May 2010, Pages 1427-1437
    http://doi:10.1016/j.neuroimage.2010.01.064
     
  • Chey et al., 2006
     
  • Eritaia et al., 2000
     
  • Biological Parametric Mapping
    Normalize DARTEL
    http://brainmap.wisc.edu/assets/normalize_DARTEL.m
     
  • Prefrontal hypoactivation and recovery in insomnia.
    Altena E; Van Der Werf YD; Sanz-Arigita EJ; Voorn TA; Rombouts SARB; Kuijer JPA; Van Someren EJW.
    Sleep 2008;31(9):1271-1276.
     
  • Design efficiency in FMRI
    http://imaging.mrc-cbu.cam.ac.uk/imaging/DesignEfficiency
     
  • E-prime paradigm for a face-name association task
     
  • MNI templates composed of 152 subject averages
    Age: mean=25.0, median=24.0, mode=19.0, stdev=4.9, range=18-44
    Sex: female=66 (43.4%), male=86 (56.6%)
    Handedness: right=129 (90.2%), left=14 (9.8%), unknown=9
     
  • CNL - Forum
    http://www.phpbbserver.com/cogneuro/index.php?mforum=cogneuro
       
  • Research on Alzheimer's disease research in the 6th and 7th EU research framework programmes (FP6 and FP7) 
    http://ec.europa.eu/health/ph_information/dissemination/diseases/alzheimer_en.htm#research
     
  • PredictAD - FP7 Project
    http://www.predictad.eu/uutiset.html?7
     
  • IXI Database
    http://www.brain-development.org/
    http://www.doc.ic.ac.uk/~dr/brain-development/downloads/
     
  • Displaying Results
    http://spect.yale.edu/displaying_results.html
     
  • A Population-Average MRI-Based Atlas Collection of the Rhesus Macaque
    McLaren DG, Kostmatka KJ, Oakes TR, Kroenke CD, Kohama SG, Matochik JA, Ingram DK, and Johnson SC. 
    Neuroimage 2009 Mar 1;45(1):52-9. Epub 2008 Nov 14
    http://www.ncbi.nlm.nih.gov/pubmed/19059346
     
  • Computational anatomy with the SPM software
    J. Ashburner
    Magn Reson Imaging. 2009 Oct;27(8):1163-74. Epub 2009 Feb 27.
     
  • Cortical activation during cholinesterase-inhibitor treatment in Alzheimer disease: preliminary findings from a pharmaco-fMRI study
    Kircher, T.T., Erb, M., Grodd, W., Leube, D.T.,
    American Journal of Geriatric Psychiatry 2005, 13, 1006–1013.
    http://www.ncbi.nlm.nih.gov/pubmed/16286445
     

Tools

MRI Classification

  • Identifying population differences in whole-brain structural networks: A machine learning approach
    Emma C. Robinson, Alexander Hammers, Anders Ericsson, A. David Edwards and Daniel Rueckert
    NeuroImage, Volume 50, Issue 3, 15 April 2010, Pages 910-919
     
  • Learning brain connectivity of Alzheimer's disease by sparse inverse covariance estimation 
    Shuai Huang, Jing Li, Liang Sun, Jieping Ye, Adam Fleisher, Teresa Wu, Kewei Chen, Eric Reiman and the Alzheimer's Disease NeuroImaging Initiative
    NeuroImage, Volume 50, Issue 3, 15 April 2010, Pages 935-949
     

Reporting rules/guidelines

  • Ten simple rules for reporting voxel-based morphometry studies
    Gerard R. Ridgway, Susie M.D. Henley, Jonathan D. Rohrer, Rachael I. Scahill, Jason D. Warren, Nick C. Fox 
    NeuroImage, Volume 40, Issue 4, 1 May 2008, Pages 1429-1435
     
  • Ten simple rules for dynamic causal modeling
    K.E. Stephan, W.D. Penny, R.J. Moran, H.E.M. den Ouden, J. Daunizeau, K.J. Friston
    NeuroImage, Volume 49, Issue 4, 15 February 2010, Pages 3099-3109
     
  • Guidelines for reporting an fMRI study 
    Russell A. Poldrack, Paul C. Fletcher, Richard N. Henson, Keith J. Worsley, Matthew Brett, Thomas E. Nichols
    NeuroImage, Volume 40, Issue 2, 1 April 2008, Pages 409-414
     

Journals

Misc.

  • NEMO Research Group
    http://web.me.com/renehurlemann/Website/Welcome.html 
     
  • Real-time functional magnetic resonance imaging: methods and applications
    Nikolaus Weiskopf, Ranganatha Sitaram, Oliver Josephs, Ralf Veit, Frank Scharnowski, Rainer Goebel, Niels Birbaumer, Ralf Deichmann and Klaus Mathiak View Abstract
    Magnetic Resonance Imaging, Volume 25, Issue 6, July 2007, Pages 989-1003
     
  • A fast diffeomorphic image registration algorithm
    Ashburner J.
    Neuroimage. 2007 Oct 15;38(1):95-113. Epub 2007 Jul 18.
    http://www.ncbi.nlm.nih.gov/pubmed/17761438
     
  • Effect of Language Switching on Arithmetic: A Bilingual fMRI Study
    Vinod Venkatraman, Soon Chun Siong, Michael W. L. Chee, Daniel Ansari. 
    Journal of Cognitive Neuroscience 2006 Jan ;18(11): p.64-74 
    http://www.fmridc.org/f/fmridc/142.html
    fMRIDC Accession Number: 2-2005-1198T
    http://files.fmridc.org/pickup/2452-DavidSmith/
     
  • Phenomenological Model of Diffuse Global and Regional Atrophy Using Finite-Element Methods
    O. Camara, M. Schweiger, R. Scahill et al
    Medical Imaging, IEEE Transactions on 25(11), pp. 1417–1430, Nov. 2006.
     
  • Imaging cerebral atrophy: normal ageing to Alzheimer’s disease
    N. C. Fox & J. M. Schott
    Lancet 363(9406), pp. 392–394, Jan 2004.
     
  • Why Sex Matters: Brain Size Independent Differences in Gray Matter Distributions between Men and Women 
    Eileen Luders, Christian Gaser, Katherine L. Narr, and Arthur W. Toga 
    Journal of Neuroscience, Nov 2009; 29: 14265 - 14270 ; doi:10.1523/JNEUROSCI.2261-09.2009
    LUDERS-VBM-GENDER.2009
     
  • Kiyoon's Lab
    http://www.nemotos.net
     
  • This ensures that subdirectories will be included in the path
    path(genpath(spm8_path), path)

     
  • http://www.nemotos.net/?p=144
     
  • http://www.fil.ion.ucl.ac.uk/spm/software/spm8/spm_update.m
     
  • Adding a final call to spm_check_installation('basic') or spm_check_installation('full')
     
  • XJview Tool
    http://www.alivelearn.net/xjview8/developers/
     
  • SPM Mouse data set
    http://www.wbic.cam.ac.uk/~sjs80/spmmouse.html
     
  • Modifying the brain activation of poor readers during sentence comprehension with extended remedial instruction: A longitudinal study of neuroplasticity 
    Meyler A, Keller TA, Cherkassky VL, Gabrieli JD, Just MA.
    Neuropsychologia. 2008 Aug;46(10):2580-2592.
    http://www.ccbi.cmu.edu/reprints/reprints.htm 
     
  • Altering Cortical Connectivity: Remediation-Induced Changes in the White Matter of Poor Readers
    Keller and Just (2009).
    Neuron, 64(5). 624-631.
     
  • Hearing faces: How the infant brain matches the face it sees with the speech it hears
    Journal of Cognitive Neuroscience, Volume 21, Issue 5, May 2009
    Davina Bristow, Ghislaine Dehaene-Lambertz, Jeremie Mattout, Catherine Soares, Teodora Gliga, Sylvain Baillet, Jean-François Mangin
    http://portal.acm.org/citation.cfm?id=1529793
     
  • There are two conventions in use in imaging: 
    Radiological -- Right will be negative 
    Neurological -- Right will be positive 
    http://www.grahamwideman.com/gw/brain/orientation/orientterms.htm
     
  • Issues in the application of the average reference: Review, critiques, and recommendations 
    Dien, J. (1998)
    Behavior Research Methods, Instruments, and Computers, 30(1), 34-43
     
  • Brain Inspired Cognitive Systems - BICS2004 
    University of Stirling, Scotland, UK
    August 29 – September 1, 2004
     
  • Nonrigid Registration of Multiple Sclerosis Brain Images Using Lesion Inpainting for Morphometry or Lesion Mapping.
    Michael Sdika and Daniel Pelletier. 
    Human Brain Mapping 30:1060–1067 (2009)"
     
  • COBRA
    http://www.fss.uu.nl/psn/web/people/personal/dumoulin/Software.html 
     
  • Freesurfer and mrVista can do retinotopy mapping
    http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis 
    http://white.stanford.edu/Software.php 
     
  • Source Localization with SPM
    https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind1001&L=SPM&P=R32210
    https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind1001&L=SPM&P=R32284
     
  • The functional anatomy of the MMN: A DCM study of the roving paradigm.
    M.I. Garrido, K.J. Friston, K.E. Stephan, S.J. Kiebel, T. Baldeweg, and J. Kilner.
    NeuroImage, 42(2):936-944, 2008.
    http://www.fil.ion.ucl.ac.uk/spm/data/eeg_mmn/ 
     
  • Against hyperacuity in brain reading: Spatial smoothing does not hurt multivariate fMRI analyses?
    Hans P. Op de Beeck
    NeuroImage, Volume 49, Issue 3, 1 February 2010, Pages 1943-1948
     
  • The Teen Brain: Insights from Neuroimaging
    J. Giedd
    Journal of Adolescent Health, Volume 42, Issue 4, Pages 335-343
     
  • Resting-state Connectivity in the Motor Cortex Independent of Seed Size
    AM Golestani, BG Goodyear
    NeuroImage, Volume 47, Supplement 1, July 2009, Page S147
     
  • Ten simple rules for dynamic causal modeling
    K.E. Stephan, W.D. Penny, R.J. Moran, H.E.M. den Ouden, J. Daunizeau, K.J. Friston
    NeuroImage, In Press, Uncorrected Proof, Available online 12 November 2009
    STEPHAN-DCM.2009.pdf
     
  • SPM compilation Linux
    http://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Linux#MEX_Required
     
  • Ten simple rules for dynamic causal modeling
    K.E. Stephan, W.D. Penny, R.J. Moran, H.E.M. den Ouden, J. Daunizeau, K.J. Friston
    NeuroImage, In Press, Uncorrected Proof, Available online 12 November 2009
    STEPHAN-DCM.2009.pdf
     
  • fMRI at 7 T: Whole-brain coverage and signal advantages even infratentorially?
    Elke R. Gizewski, Armin de Greiff, Stefan Maderwald, Dagmar Timmann, Michael Forsting, Mark E. Ladd
    NeuroImage, Volume 37, Issue 3, 1 September 2007, Pages 761-768
     
  • A New Approach for Separation of Functional MRI Images' Components Using Modified FastICA Algorithm
    Houtan Haddad Larijani, Gholamali Rezai Rad
    Fifth International Conference BioMedical Visualization: Information Visualization in Medical and Biomedical Informatics
     
  • A Comparative Study of ICA Based Approaches for Separation of Components in Functional MRI Sequences
    Gholamali Rezai Rad, Houtan Haddad Larijani
    3rd International Conference on Geometric Modeling & Imaging
     
  • ACTIVATION DETECTION IN FUNCTIONAL MRI BASED ON NON-SEPARABLE SPACE-TIME NOISE MODELS
    Joonki Noh and Victor Solo
    ISBI 2008
     
  • ROBUST CORRELATION ANALYSIS WITH AN APPLICATION TO FUNCTIONAL MRI
    Joakim Rydell, Magnus Borga, Hans Knutsson
    ICASSP 2008 
     
  • Subspace models for functional MRI data analysis
    Friman, O.;
    IEEE International Symposium on Biomedical Imaging: Nano to Macro, 2004
     
  • Ellipsoidal support vector clustering for functional MRI analysis
    Defeng Wang, Lin Shi, Daniel S. Yeung, Eric C.C. Tsang, Pheng Ann Heng
    Pattern Recognition, Volume 40, Issue 10, October 2007, Pages 2685-2695
    WANG-PR-FMRI.2007.pdf
     
  • A multistep unsupervised fuzzy clustering analysis of fMRI time series
    M. Fadili, S. Ruan, D. Bloyet, B. Mazoyer
    Human Brain Mapping 10 (2000) 160– 178.
     
  • Support vector clustering for brain activation detection
    D. Wang, L. Shi, D. S. Yeung, P.A. Heng,
    Proc. 8th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI’05), Palm Springs,USA., 2005, pp. 572–579. 
     
  • Non-linear fourier time series analysis for human brain mapping by functional magnetic resonance imaging
    N. Lange, S. Zeger
    Applied Statististics 46 (1) (1997) 1–29.
     
  • Ellipsoidal Support Vector Clustering for Functional MRI Analysis
    D Wang, L. Shi, D. Yeung, E. Tsang, and P. A. Heng
    Pattern Recognition. 2007, 40(10):2685-2695
     
  • AAL toolbox
    http://www.fil.ion.ucl.ac.uk/spm/ext/#AAL
     
  • IBASpm, an automatic labeler and you choose the 116Atlas (uses the AAL)
    http://www.thomaskoenig.ch/Lester/ibaspm.htm
     
  • ISMRM Workshops
    http://www.ismrm.org/workshops/
     
  • Centre for Cognitive Neuroimaging (CCNi)
    (Department of Psychology, University of Glasgow)
    http://www.ccni.gla.ac.uk
     
  • The Application of Subliminal Priming in Lie Detection: Scenario for Identification of Members of a Terrorist Ring
    Lui, M., & Rosenfeld, J. P. (2009)
    Psychophysiology, 46, 889-903. (impact factor: 3.32)
     
  • John Ashburner GEMs SPM
    http://www.sph.umich.edu/~nichols/JohnsGems5.html
     
  • BV-Tools - Ralf Schönmeyer (Brain Imaging Center - Frankfurt am Main)
    http://www.bic.uni-frankfurt.de/bv-tools
     
  • Automated Histogram-Based Brain Segmentation in T1-Weighted Three-Dimensional Magnetic Resonance Head Images
    Zu Y. Shan, Guang H. Yue and Jing Z. Liu
    NeuroImage, Volume 17, Issue 3, November 2002, Pages 1587-1598
    http://doi:10.1006/nimg.2002.1287 
     
  • Detection and detrending in fMRI data analysis
    Ola Friman,, Magnus Borga, Peter Lundberg and Hans Knutsson
    NeuroImage, Volume 22, Issue 2, June 2004, Pages 645-655
    http://dx.doi.org/10.1016/j.neuroimage.2004.01.033 
     
  • Motivation, Emotion, Feeding, Drinking
    Neuroreport. 13(16):2023-2026, November 15, 2002.
    Schienle, A. CA; Stark, R.; Walter, B.; Blecker, C.; Ott, U.; Kirsch, P.; Sammer, G.; Vaitl, D.
     
    Abstract: fMRI studies have shown that the perception of facial disgust expressions specifically activates the insula. The present fMRI study investigated whether this structure is also involved in the processing of visual stimuli depicting non-mimic disgust elicitors compared to fear-inducing and neutral scenes. Twelve female subjects were scanned while viewing alternating blocks of 40 disgust-inducing, 40 fear-inducing and 40 affectively neutral pictures, shown for 1.5 s each. Afterwards, affective ratings were assessed. The disgust pictures, rated as highly repulsive, induced activation in the insula, the amygdala, the orbitofrontal and occipito-temporal cortex. Since during the fear condition the insula was also involved, our findings do not fit the idea of the insula as a specific disgust processor.
     
  • Statistical parametric mapping
    K. Friston
    Statistical Parametric Mapping, 2007, Pages 10-31
    FRISTON-SPM.2007.pdf
     
  • Voxel-Based Morphometry—The Methods
    John Ashburner and Karl J. Friston
    NeuroImage 11 (6): 805–821, June 2000
    http://doi:10.1006/nimg.2000.0582
    http://www.fil.ion.ucl.ac.uk/spm/doc/papers/john_vbm_methods.pdf
     
  • Abnormal neural activity in children with attention deficit hyperactivity disorder: a resting-state functional magnetic resonance imaging study.
    Cao, Qingjiu a; Zang, Yufeng b; Sun, Li a; Sui, Manqiu a; Long, Xiangyu, Zou, Qihong, Wang, Yufeng
    Neuroreport. 17(10):1033-1036, July 17, 2006.
     
  • Regulation of anterior insular cortex activity using real-time fMRI
    Andrea Caria, Ralf Veit, Ranganatha Sitaram, Martin Lotze, Nikolaus Weiskopf, Wolfgang Grodd, Niels Birbaumer
    NeuroImage, Volume 35, Issue 3, 15 April 2007, Pages 1238-1246
    CARIA-FMRI.2007.pdf
     
  • Automated cerebrum segmentation of three-dimensional sagittal brain MR images
    H. Shin, K. Sohn, C. Lee
    Computers in Biology and Medicine, vol. 32, pp. 311-328, 2002.
     
  • Relationships between age, neuropsychological scores and structural brain measures in 236 healthy aged adults of Chinese origin
    Functional Connectivity map DARTEL
     
  • The geometry of correlation fields, with an application to functional connectivity of the brain
    Cao, J. & Worsley, K.J. (1999). 
    Annals of Applied Probability, 9:1021-1057.
     
  • Normal aging and sexual dimorphism of Japanese brain
    Goto, R., Kawashima, R., Zijdenbos, A., Neelin, P., Lerch, J., Sato, K., One, S., Nakagawa,  M., Taki, Y., Sugiura, M., Watanabe, J., Fukuda, H. & Evans, A.C. (2001).
    NeuroImage, 13:S794.
     
  • A general statistical analysis for fMRI data
    Worsley, K.J., Liao, C., Aston, J.A.D., Petre, V., Duncan, G.H., Morales, F. & Evans, A.C. (2002). 
    NeuroImage, 15:1-15.
     
  • Unified univariate and multivariate random field theory
    Worsley, K.J., Taylor, J.E., Tomaiuolo, F. & Lerch, J. (2004). 
    NeuroImage, 23:S189-195.
     
  • REST - Resting-state fMRI data analysis toolkit
    By Xiao-Wei Song and Chao-Gan Yan
    http://resting-fmri.sourceforge.net
    REST is an independent toolkit designed for resting state fMRI data analysis. It eases the analysis process with a GUI and contains three methods:
    - functional connectivity,
    - Amplitude of Low Frequency Fluctuation (ALFF)
    - Regional Homogeneity (ReHo)
     
  • Computational anatomy with the SPM software
    John Ashburner 
    Magnetic Resonance Imaging
    doi:10.1016/j.mri.2009.01.006
     
  • Illustrative Hybrid Visualization and Exploration of Anatomical and Functional Brain Data
    W. Jainek and S. Born and D. Bartz and W. Straßer and J. Fischer,
    Computer Graphics Forum (Special Issue on Eurographics Symposium on Visualization), September 2008 (Vol. 27, Issue 3)
    http://www.jainek.de/projects/iBrain/
     
  • Effect of Language Switching on Arithmetic: A Bilingual fMRI Study
    Vinod Venkatraman, Soon Chun Siong, Michael W. L. Chee, Daniel Ansari.
    Journal of Cognitive Neuroscience 2006 Jan ;18(11): p.64-74
    fMRIDC Accession Number: 2-2005-1198T
    http://www.fmridc.org/f/fmridc/142.html 
     
  • Effect of Language Switching on Arithmetic: A Bilingual fMRI Study
    Vinod Venkatraman, Soon Chun Siong, Michael W. L. Chee, Daniel Ansari.
    Journal of Cognitive Neuroscience 2006 Jan ;18(11): p.64-74
    fMRIDC Accession Number: 2-2005-1198T
    http://www.fmridc.org/f/fmridc/142.html 
     
  • Scripts to analyse the dataset available on the SPM website, that can serve as examples
    http://www.fil.ion.ucl.ac.uk/spm/data/auditory/auditory_spm5_batch.m
    http://www.fil.ion.ucl.ac.uk/spm/data/attention/attention_spm5_batch.m
    http://www.fil.ion.ucl.ac.uk/spm/data/face_rep/face_rep_spm5_batch.m
    http://www.fil.ion.ucl.ac.uk/spm/data/editfilenames.m
     
  • A sparse variational Bayesian approach for fMRI data analysis
    http://www.ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=4696632&arnumber=4696811&count=216&index=177 
     
  • % load the rp*.txt file for this run
    [motion_params_file, dirs] = spm_select('List',load_dir,'^rp*.*\.txt$');
    jobs{1}.stats{1}.fmri_spec.sess(i).multi_reg{1} = [load_dir filesep motion_params_file];
     
  • Cortical reorganization in patients with subcortical hemiparesis: neural mechanisms of functional recovery and prognostic implication
    Fujii Y, Nakada T.
    J Neurosurg. 2003 98:64--73.
     
  • Evolution of cortical activation during recovery from corticospinal tract infarction
    Marshall RS, Perera GM, Lazar RM, Krakauer JW, Constantine RC, DeLaPaz RL.
    Stroke 2000. 31:656--661.
    http://stroke.ahajournals.org/cgi/reprint/31/3/656 
    MARSHALL-STROKE.2000.pdf
     
  • Motor system activation after subcortical stroke depends on corticospinal system integrity.
    Ward NS, Newton JM, Swayne OB, Lee L, Thompson AJ, Greenwood RJ, Rothwell JC, Frackowiak RS.
    Brain 2006 129(3):809-819; doi:10.1093/brain/awl002
    http://brain.oxfordjournals.org/cgi/content/abstract/129/3/809
    WARD-STROKE.2006.pdf
      
  • https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind04&L=SPM&P=R231031
     
  • VBM5 without GUI
    http://dbm.neuro.uni-jena.de/vbm/vbm5-for-spm5/batchmode-without-gui/
     
  • WSPM: Wavelet-Based Statistical Parametric Mapping
    D. Van De Ville, M.L. Seghier, F. Lazeyras, T. Blu, M. Unser
    Neuroimage, vol. 37, no. 4, pp. 1205-1217, October 2007
     
  • Statistical Representation of High-Dimensional Deformation Fields with Application to Statistically-Constrained 3D Warping
    Xue, Shen, et al.
    Medical Image Analysis, 10:740-751, 2006
    fMRI large study using HAMMER
     
  • One of the largest longitudinal studies of aging in the world to date, (an 18-year annual follow-up of 150 elderly individuals)
  • A relatively large schizophrenia imaging study (148 participants)
     
  • A morphometric study of XXY children
    The largest imaging study of the effects of diabetes on the brain to date, (650 patients imaged twice in a 8-year period)
     
  • Coma scales
    F. Servadei
    The Lancet, Volume 367, Issue 9510, Pages 548-549
     
  • Gray and white matter flumazenil binding in neocortical epilepsy with normal MRI. A PET study in 44 patients.
    Hammers A, Koepp MJ, Richardson MP, Hurlemann R, Brooks DJ, Duncan JS.
    Brain 2003, 126: 1300-1318
     
  • Upregulation of opioid receptor binding following spontaneous epileptic seizures.
    Hammers A, Asselin MC, Hinz R, Kitchen I, Brooks DJ, Duncan JS, Koepp MJ.
    Brain 2007, 130(4): 1009-1016
     

Tools (MATLAB / SPM Toolbox)

SPM code

  • Thomas Nichols
    Karsten Specht
    Mauro Pesenti
    Tom Johnstone
    Robert Welsh
    Alexa Morcom
    Torben Ellegaard Lund
    Matthew Brett
    Daniel Kimberg
    Max Gunther
    Jesper Andersson
    Alexander Hammers
     
  • For example print -f1 -djpeg100 -r300 -noui
    'myimage.jpg' will print window 1 as a jpeg with 100% quality at a resolution of 300 dpi without the UI controls and to file myimage.jpg.
     

Methods

  • Automated image registration using a 105 parameter non-linear model
    Nancy L. Sicotte, Roger P. Woods, John C. Mazziotta
    NeuroImage, Volume 3, Issue 1, Supplement 1, June 1996, Page S123
    SICOTTE-MRI.1996.pdf
     

February 4, 2009

  • Identification of activated regions during a language task
    D. De Carli, G. Garreffa, C. Colonnese, G. Giulietti, L. Labruna, E. Briselli, S. Ken, M. Macrì, B. Maraviglia
    Magnetic Resonance Imaging, Volume 25, Issue 6, Pages 933-938
     
  • Reproducibility of activation in four motor paradigms An fMRI study
    Patrick Havel, Bernhard Braun, Sabine Rau, Joerg-Christian Tonn, Gunther Fesl, Hartmut Brückmann, Josef Ilmberger
    Journal of Neurology, Volume 253, Number 4 / April, 2006
    http://www.springerlink.com/content/y1238q4852536017/
    HAVEL-FMRI.2006.pdf
     
  • Deriving the optimal number of events for an event-related fMRI study based on the spatial extent of activation
    Kevin Murphy, Hugh Garavan
    NeuroImage, Volume 27, Issue 4, 1 October 2005, Pages 771-777
    MURPHY-FMRI.2005.pdf
     
  • An empirical investigation into the number of subjects required for an event-related fMRI study
    Kevin Murphy, Hugh Garavan
    NeuroImage, Volume 22, Issue 2, June 2004, Pages 879-885
    MURPHY-FMRI.2004.pdf
     
  • Impact of alertness training on spatial neglect: A behavioural and fMRI study
    M. Thimm, G.R. Fink, J. Küst, H. Karbe, W. Sturm
    Neuropsychologia, Volume 44, Issue 7, 2006, Pages 1230-1246
    THIMM-FMRI.2006.pdf
     
  • Functional reorganization in patients with right hemisphere stroke after training of alertness: A longitudinal PET and fMRI study in eight cases
    Sturm W, Longoni F, Weis S, Specht K, Herzog H, Vohn R, Thimm M, Willmes K.
    Neuropsychologia 2004; 42(4):434-450.
     
  • The myth of the normal, average human brain—The ICBM experience: (1) Subject screening and eligibility
    John C. Mazziotta, Roger Woods, Marco Iacoboni, Nancy Sicotte, Kami Yaden, Mary Tran, Courtney Bean, Jonas Kaplan, Arthur W. Toga and Members of the International Consortium for Brain Mapping (ICBM)
    NeuroImage, Volume 44, Issue 3, 1 February 2009, Pages 914-922
    MAZZIOTTA-MRI.2009.pdf
     
  • Functional and structural mapping of human motor systems
    Paul N. Pfeiffer, Nancy L. Sicotte, James Mattiello, Usha Sinha, Roger P. Woods, John C. Mazziotta, Jeffry R. Alger
    NeuroImage, Volume 11, Issue 5, Supplement 1, May 2000, Page S873
    PFEIFFER-MOTOR.2000.pdf
     
  • A Probabilistic Atlas of the Human Brain: Theory and Rationale for Its Development : The International Consortium for Brain Mapping (ICBM)
    John C. Mazziotta, Arthur W. Toga, Alan Evans, Peter Fox, Jack Lancaster
    NeuroImage, Volume 2, Issue 2, Part 1, June 1995, Pages 89-101
    MAZZIOTTA-MRI.1995.pdf
     
  • Neural basis of the retrieval of people's names: Evidences from brain-damaged patients and fMRI
    Tsukiura T, Fujii T, Fukatsu R, Otsuki T, Okuda J, Umetsu A, Suzuki K, Tabuchi M, Yanagawa I, Nagasaka T, Kawashima R, Fukuda H, Takahashi S, Yamadori A.
    Journal of Cognitive Neuroscience 2002 Aug ;14(6): p.922-937
     
  • Modelling large motion events in fMRI studies of patients with epilepsy
     
  • Voxel Selection in fMRI Data Analysis: A Sparse Representation Method
    Authors: Yuanqing Li, Zhuliang Yu, Praneeth Namburi, Cuntai Guan
    Paper: 2542 / Session: BISP-P1: Biomedical Imaging
    Location: Poster Area E Time: Tuesday, April 21, 17:00 - 19:00
    Topic: Bio Imaging and Signal Processing: Medical imaging
      
  • Prediction and interpretation of distributed neural activity with sparse models
    Melissa K. Carroll, Guillermo A. Cecchi, Irina Rish, Rahul Garg and A. Ravishankar Rao
    NeuroImage, Volume 44, Issue 1, 1 January 2009, Pages 112-122
     
  • Voxel-based morphometry in the detection of dysplasia and neoplasia in childhood epilepsy: Combined grey/white matter analysis augments detection .
    Jason M. Bruggemann, Marko Wilke, Seu S. Som, Ann M.E. Bye, Andrew Bleasel, John A. Lawson
    Epilepsy Research, Volume 77, Issues 2-3, December 2007, Pages 93-101
    BRUGGEMANN-VBM.2007.pdf
     
  • Automatic Segmentation of Brain Structures Based on Anatomic Atlas
    Seixas, F.L.; Damasceno, J.; da Silva, M.P.; de Souza, A.S.; Saade, D.C.M.
    Intelligent Systems Design and Applications, 2007. ISDA 2007. Seventh International Conference on
    Volume , Issue , 20-24 Oct. 2007 Page(s):329 - 334
     
  • Optimized voxel-based morphometry in children with developmental dyscalculia
    S. Rotzer, K. Kucian, E. Martin, M. von Aster, P. Klaver, T. Loenneker
    NeuroImage, Volume 39, Issue 1, 1 January 2008, Pages 417-422
    ROTZER-VBM.2008.pdf
     
  • fMRI study of problem-solving after severe traumatic brain injury
     
  • VBM Tools
    http://www.sbirc.ed.ac.uk/cyril/cp_download.html 
     
  • Dave Langers
    Neuroimage 2007 .264-273
     
  • Zaehle T
    Neuroimage 2007. 1195-1204
     
  • spm_kl_gamma
     
  • Toolbox FNC by the Calhoun group
    http://mialab.mrn.org/software/index.php
     

Data

Researchers

Cytoarchitectonic

  • A new SPM toolbox for combining probabilistic cytoarchitectonic maps and functional imaging data.
    Eickhoff S, Stephan KE, Mohlberg H, Grefkes C, Fink GR, Amunts K, Zilles K:
    NeuroImage 25(4), 1325-1335, 2005
     
  • Testing anatomically specified hypotheses in functional imaging using cytoarchitectonic maps.
    Eickhoff, S.B.; Heim, S.; Zilles, K.; Amunts, K.
    NeuroImage 32(2), 570-582, 2006
     
  • Assignment of functional activations to probabilistic cytoarchitectonic areas revisited.
    Eickhoff SB, Paus T, Caspers S, Grosbras MH, Evans A, Zilles K, Amunts K
    NeuroImage 36(3), 511-521, 2007
     

Segmentation

  • Probabilistic segmentation of brain tissue in MR imaging
    Petronella Anbeek, Koen L. Vincken, Glenda S. van Bochove, Matthias J.P. van Osch, Jeroen van der Grond
    NeuroImage, Volume 27, Issue 4, 1 October 2005, Pages 795-804
    ANBEEK-MRI.2005.pdf
     
  • Probabilistic segmentation of white matter lesions in MR imaging
    Petronella Anbeek, Koen L. Vincken, Matthias J. P. van Osch, Robertus H. C. Bisschops, Jeroen van der Grond
    NeuroImage, Volume 21, Issue 3, March 2004, Pages 1037-1044
    ANBEEK-MRI.2004.pdf
     

February 3, 2009

  • Can voxel based morphometry, manual segmentation and automated segmentation equally detect hippocampal volume differences in acute depression?
    Loretxu Bergouignan, Marie Chupin, Yvonne Czechowska, Serge Kinkingnéhun, Cédric Lemogne, Guillaume Le Bastard, Martin Lepage, Line Garnero, Olivier Colliot, Philippe Fossati
    NeuroImage, In Press, Corrected Proof, Available online 21 November 2008
     
  • Interpreting scan data acquired from multiple scanners: A study with Alzheimer's disease
    Cynthia M. Stonnington, Geoffrey Tan, Stefan Klöppel, Carlton Chu, Bogdan Draganski, Clifford R. Jack Jr., Kewei Chen, John Ashburner, Richard S.J. Frackowiak
    NeuroImage, Volume 39, Issue 3, 1 February 2008, Pages 1180-1185
     
  • International Consortium for Brain Mapping
    http://www.loni.ucla.edu/ICBM/
     
  • Brain development in children and adolescents: Insights from anatomical magnetic resonance imaging
    Rhoshel K. Lenroot, Jay N. Giedd
    Neuroscience & Biobehavioral Reviews, Volume 30, Issue 6, 2006, Pages 718-729
    http://dx.doi.org.ejproxy.a-star.edu.sg/10.1016/j.neubiorev.2006.06.001
     
  • Template-O-Matic: A toolbox for creating customized pediatric templates
    Marko Wilke, Scott K. Holland, Mekibib Altaye and Christian Gaser
    NeuroImage Volume 41, Issue 3, 1 July 2008, Pages 903-913
    http://dx.doi.org/10.1016/j.neuroimage.2008.02.056
     
  • FMRI technology and traumatic brain injury rehabilitation: Guidelines for methodological and conceptual pitfalls.
    F.G. Hillary, J. Steffener, B.B. Biswal, G. Lange, J. DeLuca, and J. Ashburner. ?
    Journal of Head Trauma Rehabilitation, 17(5):411-430, 2003
     
  • http://www.hocoma.ch/en/
     
  • Correlation of cognitive functions with voxel-based morphometry in patients with hippocampal sclerosis
    Niels K. Focke, Pam J. Thompson, John S. Duncan
    Epilepsy & Behavior, Volume 12, Issue 3, April 2008, Pages 472-476
    FOCKE-VBM.2008.pdf
     
  • Ten simple rules for reporting voxel-based morphometry studies
    Gerard R. Ridgway, Susie M.D. Henley, Jonathan D. Rohrer, Rachael I. Scahill, Jason D. Warren, Nick C. Fox
    NeuroImage, Volume 40, Issue 4, 1 May 2008, Pages 1429-1435
    RIDGWAY-VBM.2008.pdf
     
  • Neuroanatomical database of normal Japanese brains
    Kazunori Sato, Yasuyuki Taki, Hiroshi Fukuda, Ryuta Kawashima
    Neural Networks, Volume 16, Issue 9, November 2003, Pages 1301-1310
    SATO-MRI-TEMPLATE.2003.pdf
    http://dx.doi.org/10.1016/j.neunet.2003.06.004
     
  • Anatomical automatic labeling
    http://www.cyceron.fr/web/aal__anatomical_automatic_labeling.html
     
  • Automated Anatomical Labeling of Activations in SPM Using a Macroscopic Anatomical Parcellation of the MNI MRI Single-Subject Brain.
    N. Tzourio-Mazoyer, B. Landeau, D. Papathanassiou, F. Crivello, O. Etard, N. Delcroix, B. Mazoyer, and M. Joliot.
    NeuroImage 2002. 15 :273-289
     
  • Age- and Sex-related effects on the neuroanatomy of healthy elderly.
    Lemaître H, Crivello F, Grassiot B, Alpérovitch A, Tzourio C, Mazoyer BM.
    NeuroOmage 2005, 26:900-911.
    http://www.cyceron.fr/web/a_brain_atlas_for_healthy_elderly.html 
     
  • PDF and code
    http://www.ece.unm.edu/~vcalhoun/courses/fMRI_Spring07/
     
  • PDF and code
    http://gilab.udg.edu/Plone/container/publications/jaume-rigau 
     
  • Graphical display of fMRI data: visualizing multidimensional space
    R. Baumgartner, R. Somorjai
    Magnetic Resonance Imaging, Volume 19, Issue 2, February 2001, Pages 283-286
    BAUMGARTNER-FMRI.2001.pdf
     
  • Language processing during natural sleep in a 6-year-old boy as assessed by functional MRI
    Marko Wilke, Scott K. Holland, and William S. Ball, Jr.
    American Journal of Neuroradiology, 2003 January; 24(1): 42–44. 
    http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1351213  
     
  • LI-tool: A new toolbox to assess lateralization in functional MR-data
    Marko Wilke, Karen Lidzba
    Journal of Neuroscience Methods, Volume 163, Issue 1, 15 June 2007, Pages 128-136
    WILKE-FMRI-LI.2007.pdf
     
  • A combined bootstrap/histogram analysis approach for computing a lateralization index from neuroimaging data
    Marko Wilke, Vincent J. Schmithorst
    NeuroImage, Volume 33, Issue 2, 1 November 2006, Pages 522-530
    WILKE-FMRI-LI.2006.pdf 
     
  • PI, Singapore Bioimaging Consortium grant SBIC RP C-012/2006
    An integrated approach to improving measurement accuracy of Magnetic Resonance brain images to support change detection in large cohort studies
    SG $605,700. 2007-2010
    http://www3.ntu.edu.sg/home/zvitali/publications.html 
     
  • spm_imcalc_ui({'test_seg1.img','brain_test.img'},'c_test_seg1.img','i1.*i2',{[],[],[],-9});
     
  • VBM study (Maguire et al, PNAS).
     
  • Bilateral thalamic gray matter changes in patients with restless legs syndrome
    Thorleif Etgen et al
    NeuroImage Volume 24, Issue 4, 15 February 2005, Pages 1242-1247
     
  • Interpreting scan data acquired from multiple scanners: A study with Alzheimer's disease
    Cynthia M. Stonnington, Geoffrey Tan, Stefan Klöppel, Carlton Chu, Bogdan Draganski, Clifford R. Jack Jr, Kewei Chen, John Ashburner and Richard S.J. Frackowiak
    NeuroImage, Volume 39, Issue 3, 1 February 2008, Pages 1180-1185
     
  • http://www.icn.ucl.ac.uk/courses/MATLAB-Tutorials/Christian_Kaul/extract_timecourse_from_voxelsMOTION_presentation.m 
     
  • ICBM DTI
    http://www.loni.ucla.edu/ICBM/Downloads/Downloads_DTI-81.shtml 
     
  • http://www.fmrib.ox.ac.uk/fsl/data/atlas-descriptions.html 
  • https://www.mristudio.org/ 
  • http://cmrm.med.jhmi.edu/
     
  • Stereotaxic white matter atlas based on diffusion tensor imaging in an ICBM template.
    Mori S, Oishi K, Jiang H, Jiang L, Li X, Akhter K, Hua K, Faria AV, Mahmood A, Woods R, Toga AW, Pike GB, Neto PR, Evans A, Zhang J, Huang H, Miller MI, van Zijl P, Mazziotta J.
    Neuroimage. 2008 Apr 1;40(2):570-82. Epub 2008 Jan 3.
     
  • Human brain white matter atlas: identification and assignment of common anatomical structures in superficial white matter.
    Oishi K, Zilles K, Amunts K, Faria A, Jiang H, Li X, Akhter K, Hua K, Woods R, Toga AW, Pike GB, Rosa-Neto P, Evans A, Zhang J, Huang H, Miller MI, van Zijl PC, Mazziotta J, Mori S.
    Neuroimage. 2008 Nov 15;43(3):447-57. Epub 2008 Jul 18
     
  • Atlas-based whole brain white matter analysis using Large Deformation Diffeomorphic Metric Mapping: Application to normal elderly and Alzheimer’s disease participants.
    Kenichi Oishi, Andreia Faria, Hangyi Jiang, Xin Li, Kazi Akhter, Jiangyang Zhang, John T. Hsu, Michael I. Miller, Peter C.M. van Zijl, Marilyn Albert, Constantine G. Lyketsos, Roger Woods, Arthur W. Toga, G. Bruce Pike, Pedro Rosa-Neto, Alan Evans, John Mazziotta, Susumu Mori
     

PCA-based

  • Principal component analysis of the dynamic response measured by fMRI: a generalized linear systems framework
    Anders H. Andersen, Don M. Gash, Malcolm J. Avison
    Magnetic Resonance Imaging, Volume 17, Issue 6, July 1999, Pages 795-815
    ANDERSEN-FMRI-PCA.1999.pdf
     
  • A novel local PCA-Based method for detecting activation signals in fMRI
    Shang-Hong Lai, Ming Fang
    Magnetic Resonance Imaging, Volume 17, Issue 6, July 1999, Pages 827-836
    LAI-FMRI-PCA.1999.pdf 
     

January 2009

December 2008

  • A new SPM toolbox for combining probabilistic cytoarchitectonic maps and functional imaging data
    Simon B. Eickhoff, Klaas E. Stephan, Hartmut Mohlberg, Christian Grefkes, Gereon R. Fink, Katrin Amunts, Karl Zilles
    NeuroImage, Volume 25, Issue 4, 1 May 2005, Pages 1325-1335
    EICKHOFF-FMRI-ATLAS.2005.pdf
     
  • Pattern of brain atrophy in elderly patients with depression revealed by voxel-based morphometry
    Karl Egger, Michael Schocke, Elisabeth Weiss, Simone Auffinger, Regina Esterhammer, Georg Goebel, Thomas Walch, Sergei Mechtcheriakov, Josef Marksteiner
    Psychiatry Research: Neuroimaging, Volume 164, Issue 3, 30 December 2008, Pages 237-244
    EGGER-VBM.2008.pdf
     
  • Improved agreement between Talairach and MNI coordinate spaces in deep brain regions
    Patrick S. Carmack, Jeff Spence, Richard F. Gunst, William R. Schucany, Wayne A. Woodward, Robert W. Haley
    NeuroImage, Volume 22, Issue 1, May 2004, Pages 367-371
    CARMACK-FMRI-ATLAS.2005.pdf
     
  • Guidelines for reporting an fMRI study
    Russell A. Poldrack, Paul C. Fletcher, Richard N. Henson, Keith J. Worsley, Matthew Brett, Thomas E. Nichols
    NeuroImage, Volume 40, Issue 2, 1 April 2008, Pages 409-414
    POLDRACK-FMRI.2008.pdf 
     
  • Lesion identification using unified segmentation-normalisation models and fuzzy clustering
    Seghier,M.L., Ramlackhansingh,A., Crinion,J., Leff,A.P., Price,C.J. (2008).
    NeuroImage 41(4), 1253-1266. ISSN: 1053-8119
     
  • Automatic classification of MR scans in Alzheimer's disease.
    Kloppel,S., Stonnington,C.M., Chu,C., Draganski,B., Scahill,R.I., Rohrer,J.D., Fox,N.C., Jack,C.R., Ashburner,J., Frackowiak,R.S. (2008).
    Brain 131(3), 681-689. ISSN: 0006-8950
    KLOPPEL-MRI-AD.2008
     
  • Voxel-based cortical thickness measurements in MRI.
    Hutton,C., De Vita,E., Ashburner,J., Deichmann,R., Turner,R. (2008).
    NeuroImage 40(4), 1701-1710. ISSN: 1053-8119
    http://www.fil.ion.ucl.ac.uk/Research/publications.html 
     
  • Brain activation for consonants and vowels.
    Carreiras,M., Price,C.J. (2008)
    Cerebral Cortex 18(7), 1727-1735. ISSN: 1047-3211
     
  • FMRI activity patterns in human LOC carry information about object exemplars within category
    Eger,E., Ashburner,J., Haynes,J.D., Dolan,R.J., Rees,G. (2008).
    Journal of Cognitive Neuroscience 20(2), 356-370. ISSN: 0898-929X
     
  • Cumulative effect of anatomical risk factors for schizophrenia: an MRI study
    Leonard, C. M., Kuldau, J. M., Breier, J. I., Zuffante, P. A., Gautier, E. R., Heron, D.-C., Lavery, E. M., Packing, J., Williams, S. A., & DeBose, C. A. (1999). 
    Biological Psychiatry, 46, 374-382
     
  • A nonparametric method for automatic correction of intensity nonuniformity in MRI data
    Sled, J. G., Zijdenbos, A. P., & Evans, A. C. (1998).
    IEEE Transactions on Medical Imaging, 17, 87-97
     
  • The Functional Magnetic Resonance Imaging Data Center (fMRIDC): the challenges and rewards of large-scale databasing of neuroimaging studies.
    Van Horn, J. D., Grethe, J. S., Kostelec, P., Woodward, J. B., Aslam, J., Rus, D., Rockmore, D., & Gazzaniga, M. S. (2001).
    Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences B, 356, 1323-1339.
     
  • Hemispheric shape of European and Japanese brains: 3-D MRI analysis of intersubject variability, ethnical, and gender differences.
    Zilles, K., Kawashima, R., Dabringhaus, A., Fukuda, H., & Schormann, T. (2001).
    Neuroimage, 13, 262-271.
     
  • Implementation of icbm2tal in BrainMap
    http://brainmap.org/icbm2tal/index.html#Download
     
  • ICBM
    http://loni.ucla.edu/icbm
     
  • Auditory-Motor Interaction Revealed by fMRI: Speech, Music, and Working Memory in Area Spt
    Hickok G, Buchsbaum B, Humphries C, Muftuler T.
    Journal of Cognitive Neuroscience 2003 Jul ;15(5): p.673-682
    fMRIDC Accession Number: 2-2003-113H8
    http://www.fmridc.org/f/fmridc/74.html 
     
  • http://en.wikipedia.org/wiki/Agile_software_development 
     
  • fMRIdc sitemap
    http://www.fmridc.org/f/fmridc/sitemap.html 
     
  • Voxel Compression mapping separates expansion and contraction before smoothing
    Scahill et al (2002)
    PNAS 99:4703-4707
     
  • Longitudinal VBM multiplies longitudinal volume change with baseline or average grey matter density
    Chételat et al (2005) NeuroImage 27:934-946
     
  • All modulation, no gray matter
    Jacobian determinant "Tensor" Based Morphometry
    Davatzikos et al. (1996) JCAT 20:88-97
     
  • Deformation field morphometry
    Cao and Worsley (1999) Ann Stat 27:925-942
     
  • Ashburner et al (1998) Hum Brain Mapp 6:348-357
     
  • Other variations on TBM
    Chung et al (2001)
    NeuroImage 14:595-606
     
  • Unified Segmentation
    Ashburner and Friston.
    NeuroImage 26(3), 2005
     
  • A Fast Diffeomorphic Image Registration Algorithm.
    Ashburner
    Neuroimage 38(1), 2007
     
  • M Chung 
    http://www.stat.wisc.edu/~mchung/publications.html
     
  • ArtRepair Software - Algorithms and software are designed toimprove the accuracy of effect size estimation for fMRI data from high motion clinical subjects
    http://cibsr.stanford.edu/tools/ArtRepair/ArtRepair.htm
     
  • http://www.fmrib.ox.ac.uk/analysis/research/possum/
     
  • Is it necessary to choose p<0.001(uncorr.) value for thresholding ?
    Can I use or is it appropriate to use a less strict threshold like p<0.05?
     

September 2008

  • Functional phantom for fMRI: a feasibility study
    Ville Renvall, Raimo Joensuu, Riitta Hari
    Magnetic Resonance Imaging, Volume 24, Issue 3, April 2006, Pages 315-320
    http://dx.doi.org.ejproxy.a-star.edu.sg/10.1016/j.mri.2005.07.012
      
  • Localization of Cardiac-Induced Signal Change in fMRI
    Mandeep S. Dagli, John E. Ingeholm, James V. Haxby
    NeuroImage, Volume 9, Issue 4, April 1999, Pages 407-415
     
  • SmartPhantom — an fMRI simulator
    Hu Cheng, Qun Zhao, George R. Duensing, Williams A. Edelstein, Diana Spencer, Nick Browne, Charles Saylor, Mark Limkeman
    Magnetic Resonance Imaging, Volume 24, Issue 3, April 2006, Pages 301-313
     
  • Ethical issues in the clinical application of fMRI: Factors affecting the validity and interpretation of activations
    John E. Desmond, S. H. Annabel Chen
    Brain and Cognition, Volume 50, Issue 3, December 2002, Pages 482-497
     
  • fMRI activation maps based on the NN-ARx model
    J. Riera, J. Bosch, O. Yamashita, R. Kawashima, N. Sadato, T. Okada, T. Ozaki
    NeuroImage, Volume 23, Issue 2, October 2004, Pages 680-697
    http://dx.doi.org.ejproxy.a-star
     
  • Chapter on Medical Applications, CAT, MRI, Ultrasound, Heart Models, Brain Models continues in Brain, Cortex, Brain Waves, EEG Analysis
    http://www.visionbib.com/bibliography/medical881.html 
     
  • Zvitali NTU Accounts
    http://web.mysites.ntu.edu.sg/zvitali/publications/documents/Forms/AllItems.aspx
     

Tutorials

April 2010 - BHC