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| '''... Brainstorm''' | '''Brainstorm''' |
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| '''... forward models''' | '''Forward models''' |
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| '''... inverse methods''' | '''Inverse methods''' |
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| '''... proprocessing''' | '''Preprocessing''' |
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| * Good practice: Gross et al. 2013 | |
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| ''' ... the default anatomy''' | '''Time-frequency''' |
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| * Colin27: MNI brain with a 1mm resolution. [[http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach|More info....]] | * Morlet wavelets: Bertrand et al. 2000 / Pantazis et al. 2005b * ERS/ERD: Pfurtscheller 1992 |
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| '''... FreeSurfer''' | '''Statistical analysis''' |
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| * Whether you are using FreeSurfer for the T1 segmentation, 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. | * Non-parametric tests: Pantazis et al., 2005a * Decoding: Cichy et al. 2014 |
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| '''... statistical analysis using non-parametric permutation tests''' | ''' Default anatomy''' |
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| * Permutation tests: Pantazis et al., 2005. | * 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]] |
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| '''... the tutorial datasets''' | '''MRI segmentation''' |
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| * TODO | * 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 '''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]] |
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| * 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 * 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 |
* 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 |
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| * 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 * 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 |
* 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 |
| Line 56: | Line 82: |
| * 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 | * 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 |
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| * Pantazis D, Nichols TE, Baillet S, Leahy RM (2005)<<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 | * 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 |
| Line 60: | Line 86: |
| * 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 |
|
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| * Uusitalo MA, Ilmoniemi RJ (1997)<<BR>>[[https://link.springer.com/article/10.1007%2FBF02534144?LI=true|Signal-space projection method for separating MEG or EEG into components]]<<BR>>Med. Biol. Eng. Comput. 35, 135–140 | * 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 |
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
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
Inverse methods
- Tikhonov-regularized inimum norm: Baillet et al., 2001
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
- Decoding: Cichy et al. 2014
Default anatomy
MNI/ICBM152: Fonov et al. 2009 | more information
MNI/Colin27: more information
BCI-DNI_BrainSuite_2016: more information
USCBrain: more information
Infant7w: Kabdebon et al. 2014
Oreilly_1y: Li et al. 2015, Shi et al. 2011
MRI segmentation
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 (registration page) and cite the appropriate references
BrainSuite: Shattuck et al. 2002
- BrainVISA: Rivière et al. 2003
Tutorial datasets
Introduction (auditory CTF MEG): more information
Group analysis (visual Elekta MEG): more information
EEG/Epilepsy: contact the authors
SEEG/Epilepsy: contact the authors
CTF MEG phantom: more information
Elekta MEG phantom: more information
OMEGA: more information
HCP-MEG: more information
Publications
The previous citations refer to the following publications. Further reading is available in the Publications section.
Baillet S, Mosher JC, Leahy RM (2001)
Electromagnetic Brain Mapping (pdf)
IEEE Signal Processing Magazine, 18(6): 14-30, Nov 2001Bertrand O, Tallon-Baudry C (2000)
Oscillatory gamma activity in humans: a possible role for object representation
Int J Psychophysiol, 38(3):211-23Cichy RM, Pantazis D, Oliva A (2014)
Resolving human object recognition in space and time
Nature neuroscience, 17:455Dale AM, Liu AK, Fischl BR, Buckner RL, Belliveau JW, Lewine JD, Halgren E (2000)
Dynamic statistical parametric mapping: combining fMRI and MEG for high-resolution imaging of cortical activity
Neuron, Apr 2000, 26(1):55-67Dale AM, Fischl B, Sereno MI (1999)
Cortical surface-based analysis (pdf)
NeuroImage 9, 179–194. doi: 10.1006/nimg.1998.0395Fonov VS, Evans AC, McKinstry RC, Almli CR, Collins DL (2009)
Unbiased nonlinear average age-appropriate brain templates from birth to adulthood
NeuroImage 47(Suppl. 1):S102. doi: 10.1016/S1053-8119(09)70884-5Gross J, Baillet S, Barnes GR, Henson RN, Hillebrand A, Jensen O, et al (2013)
Good practice for conducting and reporting MEG research
NeuroImage 65, 349–363Gramfort A, Papadopoulo T, Olivi E, Clerc M (2010)
OpenMEEG: opensource software for quasistatic bioelectromagnetics
BioMedical Engineering OnLine 45:9, 2010Huang MX, Mosher JC, Leahy RM (1999)
A sensor-weighted overlapping-sphere head model and exhaustive head model comparison for MEG (pdf)
Phys Med Biol, 44:423-440Kabdebon C, Leroy F, Simmonet H, Perrot M, Dubois J, Dehaene-Lambertz G
Anatomical correlations of the international 10–20 sensor placement system in infants
NeuroImage, 1 Oct 2014, 99:342-356Kybic J, Clerc M, Abboud T, Faugeras O, Keriven R, Papadopoulo T (2005)
A common formalism for the integral formulations of the forward EEG problem (pdf)
IEEE Transactions on Medical Imaging, 24:12-28, 2005Leahy RM, Mosher JC, Spencer ME, Huang MX, Lewine JD (1998)
A study of dipole localization accuracy for MEG and EEG using a human skull phantom (pdf)
Electroencephalography and Clinical Neurophysiology, 107(2):159-73, 1998Makeig S, Bell AJ, Jung TP, Sejnowski TJ (1996)
Independent component analysis of electroencephalographic data
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.Mosher, Leahy RM, Lewis PS (1999)
EEG and MEG: Forward solutions for inverse methods (pdf)
IEEE Trans Biomedical Eng, 46(3):245-259, Mar 1999Niso G, Tadel F, Bock E, Cousineau M, Santos A, Baillet S (2019)
Brainstorm Pipeline Analysis of Resting-State Data from the Open MEG Archive
Frontiers in Neuroscience, Mar 2019Pantazis D, Nichols TE, Baillet S, Leahy RM (2005a)
A Comparison of Random Field Theory and Permutation Methods for the Statistical Analysis of MEG data (pdf)
Neuroimage, 25(2):383-394, 2005Pascual-Marqui RD (2002)
Standardized low-resolution brain electromagnetic tomography (sLORETA): technical details
Methods Find Exp Clin Pharmacol 2002, 24 Suppl D:5-12Pfurtscheller G (1992)
Event-related synchronization (ERS): an electrophysiological correlate of cortical areas at rest
Electroencephalogr Clin Neurophysiol, 83(1):62-9Rivière D, Régis J, Cointepas Y, Papadopoulos-Orfanos D, Cachia A, Mangin JF (2003)
A freely available anatomist/brainVISA package for structural morphometry of the cortical sulci
in Proceedings of the 9th HBM, Neuroimage, Vol. 19Shattuck D W, Leahy RM (2002)
Brainsuite: an automated cortical surface identification tool
Med. Image Anal. 6, 129–142. doi: 10.1016/S1361-8415(02)00054-3Tadel F, Baillet S, Mosher JC, Pantazis D, Leahy RM (2011)
Brainstorm: A User-Friendly Application for MEG/EEG Analysis
Computational Intelligence and Neuroscience, vol. 2011, Article ID 879716, 13 pages, 2011. doi:10.1155/2011/879716Tadel F, Bock E, Niso G, Mosher JC, Cousineau M, Pantazis D, Leahy RM, Baillet S (2019)
MEG/EEG Group Analysis With Brainstorm
Frontiers in Neuroscience, Feb 2019Uusitalo MA, Ilmoniemi RJ (1997)
Signal-space projection method for separating MEG or EEG into components
Med. Biol. Eng. Comput. 35, 135–140