= Cite Brainstorm in your publications = Once you are done with your analyses performed with Brainstorm, proper citation would be greatly appreciated; thank you! == How to cite... == '''Brainstorm''' * To include in all your publications using Brainstorm: <<BR>>Data analysis was performed with Brainstorm '''(Tadel et al. 2011)''', which is documented and freely available for download online under the GNU general public license (http://neuroimage.usc.edu/brainstorm). * Group analysis processing pipeline: Tadel et al. 2019 * Resting state processing pipeline: Niso et al. 2019 '''Forward models''' * Spherical head model: Mosher et al. 1999 * Overlapping spheres: Huang et al. 1999 * OpenMEEG BEM: Gramfort et al. 2010 / Kybic et al. 2005 * Duneuro FEM: [[https://www.sciencedirect.com/science/article/pii/S1053811922009727|Medani et al. 2022]] '''Inverse methods''' * Tikhonov-regularized inimum norm: Baillet et al., 2001 [[http://neuroimage.usc.edu/paperspdf/BailletMosherLeahy_IEEESPMAG_Nov2001.pdf|Electromagnetic brain mapping]], IEEE SP MAG 2001. * dSPM: Dale et al. 2000 * sLORETA: Pascual-Marqui 2002 '''Preprocessing''' * SSP: Uusitalo et al. 1999 * ICA: Makeig et al. 1996 * Good practice: Gross et al. 2013 '''Time-frequency''' * Morlet wavelets: Bertrand et al. 2000 / Pantazis et al. 2005b * ERS/ERD: Pfurtscheller 1992 '''Statistical analysis''' * Non-parametric tests: Pantazis et al., 2005a * FieldTrip cluster-based tests: Maris and Oostenveld, 2007 * Decoding: Cichy et al. 2014 ''' Default anatomy''' * MNI/ICBM152: Fonov et al. 2009 | [[http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009|more information]] * MNI/Colin27: [[http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27|more information]] * BCI-DNI_BrainSuite_2016: [[http://brainsuite.org/svreg_atlas_description/|more information]] * USCBrain: [[http://brainsuite.org/uscbrain-description/|more information]] * Infant7w: [[http://www.sciencedirect.com/science/article/pii/S105381191400411X|Kabdebon et al. 2014]] * Oreilly_1y: [[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127322|Li et al. 2015]], [[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018746|Shi et al. 2011]] '''MRI processing''' * FreeSurfer: Whether you are using FreeSurfer for the T1 segmentation (Dale et al. 1999), the cortical atlases or the FSAverage subject default: please register on their website ([[https://surfer.nmr.mgh.harvard.edu/registration.html|registration page]]) and cite the appropriate references * BrainSuite: Shattuck et al. 2002 * BrainVISA: Rivière et al. 2003 * MNI normalization (SPM): Ashburner and Friston, 2005 * MRI coregistration (SPM): Ashburner and Friston, 2005 '''Tutorial datasets''' * Introduction (auditory CTF MEG): [[https://neuroimage.usc.edu/brainstorm/Tutorials/ChannelFile#DatasetIntroduction.License|more information]] * Group analysis (visual Elekta MEG): [[https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle#License|more information]] * EEG/Epilepsy: [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy#DatasetEpilepsy.License|contact the authors]] * SEEG/Epilepsy: [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity#DatasetEpileptogenicity.License|contact the authors]] * CTF MEG phantom: [[https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomCtf#License|more information]] * Elekta MEG phantom: [[https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomElekta#License|more information]] * OMEGA: [[https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega#OMEGA_database|more information]] * HCP-MEG: [[https://neuroimage.usc.edu/brainstorm/Tutorials/HCP-MEG#License|more information]] == References == The previous citations refer to the following publications. Further reading is available in the [[Pub|Publications]] section. * Ashburner J, Friston KJ (2005)<<BR>>[[https://www.sciencedirect.com/science/article/pii/S1053811905001102?via=ihub|Unified segmentation]]<<BR>>NeuroImage 26, 839–851. doi: 10.1016/j.neuroimage.2005.02.018 * Baillet S, Mosher JC, Leahy RM (2001)<<BR>>[[https://ieeexplore.ieee.org/document/962275|Electromagnetic Brain Mapping]] ([[http://neuroimage.usc.edu/paperspdf/BailletMosherLeahy_IEEESPMAG_Nov2001.pdf|pdf]])<<BR>>IEEE Signal Processing Magazine, 18(6): 14-30, Nov 2001 * Bertrand O, Tallon-Baudry C (2000)<<BR>>[[http://www.iec-lnc.ens.fr/IMG/Files/Visual/Publications/2000_Review_IntJPsychol.pdf|Oscillatory gamma activity in humans: a possible role for object representation]]<<BR>>Int J Psychophysiol, 38(3):211-23 * Cichy RM, Pantazis D, Oliva A (2014)<<BR>>[[https://www.nature.com/articles/nn.3635|Resolving human object recognition in space and time]]<<BR>>Nature neuroscience, 17:455 * Dale AM, Liu AK, Fischl BR, Buckner RL, Belliveau JW, Lewine JD, Halgren E (2000)<<BR>> [[http://www.ncbi.nlm.nih.gov/pubmed/10798392|Dynamic statistical parametric mapping: combining fMRI and MEG for high-resolution imaging of cortical activity]]<<BR>>Neuron, Apr 2000, 26(1):55-67 * Dale AM, Fischl B, Sereno MI (1999)<<BR>>[[https://www.sciencedirect.com/science/article/pii/S1053811998903950|Cortical surface-based analysis]] ([[http://www-cogsci.ucsd.edu/~sereno/papers/CorticalSurface99a.pdf|pdf]])<<BR>>NeuroImage 9, 179–194. doi: 10.1006/nimg.1998.0395 * Fonov VS, Evans AC, McKinstry RC, Almli CR, Collins DL (2009)<<BR>>[[https://www.infona.pl/resource/bwmeta1.element.elsevier-22edcca2-af85-3025-a371-3f49c018e71f|Unbiased nonlinear average age-appropriate brain templates from birth to adulthood]]<<BR>>NeuroImage 47(Suppl. 1):S102. doi: 10.1016/S1053-8119(09)70884-5 * Gross J, Baillet S, Barnes GR, Henson RN, Hillebrand A, Jensen O, et al (2013)<<BR>>[[https://www.sciencedirect.com/science/article/pii/S1053811912009895|Good practice for conducting and reporting MEG research]]<<BR>>NeuroImage 65, 349–363 * Gramfort A, Papadopoulo T, Olivi E, Clerc M (2010)<<BR>>[[http://www.biomedical-engineering-online.com/content/9/1/45|OpenMEEG: opensource software for quasistatic bioelectromagnetics]]<<BR>>BioMedical Engineering OnLine 45:9, 2010 * Huang MX, Mosher JC, Leahy RM (1999)<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/10070792|A sensor-weighted overlapping-sphere head model and exhaustive head model comparison for MEG]] ([[http://neuroimage.usc.edu/paperspdf/PMB99.pdf|pdf]])<<BR>>Phys Med Biol, 44:423-440 * Kabdebon C, Leroy F, Simmonet H, Perrot M, Dubois J, Dehaene-Lambertz G<<BR>>[[https://www.sciencedirect.com/science/article/pii/S105381191400411X|Anatomical correlations of the international 10–20 sensor placement system in infants]]<<BR>>NeuroImage, 1 Oct 2014, 99:342-356 * Kybic J, Clerc M, Abboud T, Faugeras O, Keriven R, Papadopoulo T (2005)<<BR>>[[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=30034&arnumber=1375158&count=10&index=1|A common formalism for the integral formulations of the forward EEG problem]] ([[ftp://ftp-sop.inria.fr/odyssee/Publications/2005/kybic-clerc-etal:05.pdf|pdf]])<<BR>>IEEE Transactions on Medical Imaging, 24:12-28, 2005 * Leahy RM, Mosher JC, Spencer ME, Huang MX, Lewine JD (1998)<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/9751287|A study of dipole localization accuracy for MEG and EEG using a human skull phantom]] ([[http://neuroimage.usc.edu/paperspdf/Phantom_Ver2.pdf|pdf]])<<BR>>Electroencephalography and Clinical Neurophysiology, 107(2):159-73, 1998 * Makeig S, Bell AJ, Jung TP, Sejnowski TJ (1996)<<BR>>[[http://papers.nips.cc/paper/1091-independent-component-analysis-of-electroencephalographic-data.pdf|Independent component analysis of electroencephalographic data]]<<BR>>in Advances in Neural Information Processing Systems. Vol. 8, eds D. S. Touretzky, M. C. Mozer, and M. E. Hasselmo (Cambridge, MA: MIT Press), 145–151. * Maris E, Oostendveld R<<BR>>[[http://www.sciencedirect.com/science/article/pii/S0165027007001707|Nonparametric statistical testing of EEG- and MEG-data]]<<BR>>J Neurosci Methods (2007), 164(1):177-90. * Mosher, Leahy RM, Lewis PS (1999)<<BR>>[[https://www.ncbi.nlm.nih.gov/pubmed/10097460|EEG and MEG: Forward solutions for inverse methods]] ([[http://neuroimage.usc.edu/paperspdf/IEEEBME99.pdf|pdf]])<<BR>>IEEE Trans Biomedical Eng, 46(3):245-259, Mar 1999 * Niso G, Tadel F, Bock E, Cousineau M, Santos A, Baillet S (2019)<<BR>>[[https://www.frontiersin.org/articles/10.3389/fnins.2019.00284/abstract|Brainstorm Pipeline Analysis of Resting-State Data from the Open MEG Archive]]<<BR>>Frontiers in Neuroscience, Mar 2019 * Pantazis D, Nichols TE, Baillet S, Leahy RM (2005a)<<BR>>[[https://www.sciencedirect.com/science/article/pii/S1053811904005671|A Comparison of Random Field Theory and Permutation Methods for the Statistical Analysis of MEG data]] ([[http://neuroimage.usc.edu/paperspdf/Pantazis_Permutations_NeuroImage.pdf|pdf]])<<BR>>Neuroimage, 25(2):383-394, 2005 * Pascual-Marqui RD (2002)<<BR>>[[http://www.ncbi.nlm.nih.gov/pubmed/12575463|Standardized low-resolution brain electromagnetic tomography (sLORETA): technical details]]<<BR>>Methods Find Exp Clin Pharmacol 2002, 24 Suppl D:5-12 * Pfurtscheller G (1992)<<BR>>[[http://www.sciencedirect.com/science/article/pii/0013469492901333|Event-related synchronization (ERS): an electrophysiological correlate of cortical areas at rest]]<<BR>>Electroencephalogr Clin Neurophysiol, 83(1):62-9 * Rivière D, Régis J, Cointepas Y, Papadopoulos-Orfanos D, Cachia A, Mangin JF (2003)<<BR>>[[https://insights.ovid.com/neuroimage/neuima/2003/06/001/freely-available-anatomist-brainvisa-package/927/00042393|A freely available anatomist/brainVISA package for structural morphometry of the cortical sulci]]<<BR>>in Proceedings of the 9th HBM, Neuroimage, Vol. 19 * Shattuck D W, Leahy RM (2002)<<BR>>[[https://www.sciencedirect.com/science/article/abs/pii/S1361841502000543|Brainsuite: an automated cortical surface identification tool]]<<BR>>Med. Image Anal. 6, 129–142. doi: 10.1016/S1361-8415(02)00054-3 * Tadel F, Baillet S, Mosher JC, Pantazis D, Leahy RM (2011)<<BR>>[[http://www.hindawi.com/journals/cin/2011/879716/|Brainstorm: A User-Friendly Application for MEG/EEG Analysis]]<<BR>>Computational Intelligence and Neuroscience, vol. 2011, Article ID 879716, 13 pages, 2011. doi:10.1155/2011/879716'' '' * Tadel F, Bock E, Niso G, Mosher JC, Cousineau M, Pantazis D, Leahy RM, Baillet S (2019)<<BR>>[[https://www.frontiersin.org/articles/10.3389/fnins.2019.00076/full?&utm_source=Email_to_authors_&utm_medium=Email&utm_content=T1_11.5e1_author&utm_campaign=Email_publication&field=&journalName=Frontiers_in_Neuroscience&id=435877#note13|MEG/EEG Group Analysis With Brainstorm]]<<BR>>Frontiers in Neuroscience, Feb 2019 * Uusitalo MA, Ilmoniemi RJ (1997)<<BR>>[[https://link.springer.com/article/10.1007/BF02534144?LI=true|Signal-space projection method for separating MEG or EEG into components]]<<BR>>Med. Biol. Eng. Comput. 35, 135–140