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| Once you are done with your analysis, please do not forget about us in the redaction of your publications... | Once you are done with your analyses performed with Brainstorm, proper citation would be greatly appreciated; thank you! |
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| == How to cite == '''To cite Brainstorm:''' |
== How to cite... == '''... Brainstorm''' |
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| * 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 |
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* Data analysis was performed with Brainstorm (Mosher et al. 2005), which is documented and freely available for download online under the GNU general public license ([[|http://neuroimage.usc.edu/brainstorm]]). '''To cite forward modeling:''' |
'''... forward models''' |
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| * Boundary Element Method: Mosher et al. 1999 | * OpenMEEG BEM: Gramfort et al., 2010 / Kybic et al., 2005 |
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| '''To cite inverse methods:''' |
'''... inverse methods''' |
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| * LCMV Beamformer: Baillet et al., 2001 | |
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| ''' To cite the default anatomy:''' | ''' ... the default anatomy''' |
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| * Colin27: MNI brain with a 1mm resolution. [[http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach|More info....]] | |
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| '''... FreeSurfer''' | |
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| * Default MRI: MNI/Colin27 brain with a 1mm resolution. [[http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach|More info....]] * Cortex, cerebellum and white matter surfaces extracted with BrainVISA software * Scalp surface comes from MNE software (fsaverage) |
* 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. |
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| '''To cite statistical analysis using the permutation tests:''' |
'''... statistical analysis using non-parametric permutation tests''' |
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| '''... the tutorial datasets''' * TODO |
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| The previous citations refers to the following publications. More publications available in the [[Pub|Publications]] section. | The previous citations refer to the following publications. Further reading is available in the [[Pub|Publications]] section. |
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| * Baillet S, Mosher JC, Leahy RM (2001)<<BR>>Electromagnetic Brain Mapping<<BR>>IEEE Signal Processing Magazine, 18(6): 14-30, Nov 2001 * 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>>[[http://neuroimage.usc.edu/paperspdf/PMB99.pdf|A sensor-weighted overlapping-sphere head model and exhaustive head model comparison for MEG]]<<BR>>Phys Med Biol, 44:423-440 * Kybic J, Clerc M, Abboud T, Faugeras O, Keriven R, Papadopoulo T (2005)<<BR>>A common formalism for the integral formulations of the forward EEG problem<<BR>>[[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=30034&arnumber=1375158&count=10&index=1|IEEE Transactions on Medical Imaging, 24:12-28, 2005.]] [[ftp://ftp-sop.inria.fr/odyssee/Publications/2005/kybic-clerc-etal:05.pdf|[pdf]]] * Leahy RM, Mosher JC, Spencer ME, Huang MX, Lewine JD (1998)<<BR>>[[http://neuroimage.usc.edu/paperspdf/Phantom_Ver2.pdf|A study of dipole localization accuracy for MEG and EEG using a human skull phantom]]<<BR>>Electroencephalography and Clinical Neurophysiology, 107(2):159-73 * Mosher, Leahy RM, Lewis PS (1999)<<BR>>[[http://neuroimage.usc.edu/paperspdf/IEEEBME99.pdf|EEG and MEG: Forward solutions for inverse methods]]<<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 (2005)<<BR>>A Comparison of Random Field Theory and Permutation Methods for the Statistical Analysis of MEG data<<BR>>Neuroimage, 25(2):383-394, 2005 * 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'' '' |
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* J.C. Mosher, S. Baillet, F. Darvas, D. Pantazis , E.K. Yildirim, R.M. Leahy, “BrainStorm Electromagnetic Imaging Software”, 5th International Symposium on Noninvasive Functional Source Imaging within the Human Brain and Heart (NFSI 2005), Minnesota, May 12-15, 2005. * M.X. Huang, J.C. Mosher and R.M. Leahy, "A sensor-weighted overlapping-sphere head model and exhaustive head model comparison for MEG",Physics in Medicine and Biology, 44(2): 423-440, Feb. 1999. * S. Baillet, J.C. Mosher, R.M. Leahy, "Electromagnetic Brain Mapping", IEEE Signal Processing Magazine, 18(6): 14-30, Nov 2001. * D. Pantazis, T. E Nichols, S. Baillet, RM Leahy, A Comparison of Random Field Theory and Permutation Methods for the Statistical Analysis of MEG data, Neuroimage, 25(2):383-394, 2005 * J.C. Mosher, R.M. Leahy, and P.S. Lewis, “EEG and MEG: Forward solutions for inverse methods,” IEEE Trans. Biomed. Eng., vol. 46, pp. 245-259, 1999. |
* 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 |
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 minimum-norm: Baillet et al., 2001.
Default value for Tikhonov parameter is λ = 10% of maximum singular value of the lead field.
... the default anatomy
Colin27: MNI brain with a 1mm resolution. More info....
... FreeSurfer
Whether you are using FreeSurfer for the T1 segmentation, the cortical atlases or the FSAverage subject default: please register on their website (registration page) and cite the appropriate references.
... statistical analysis using non-parametric permutation tests
- Permutation tests: Pantazis et al., 2005.
... the tutorial datasets
- TODO
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
IEEE Signal Processing Magazine, 18(6): 14-30, Nov 2001Gramfort 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
Phys Med Biol, 44:423-440Kybic J, Clerc M, Abboud T, Faugeras O, Keriven R, Papadopoulo T (2005)
A common formalism for the integral formulations of the forward EEG problem
IEEE Transactions on Medical Imaging, 24:12-28, 2005. [pdf]Leahy 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
Electroencephalography and Clinical Neurophysiology, 107(2):159-73Mosher, Leahy RM, Lewis PS (1999)
EEG and MEG: Forward solutions for inverse methods
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 (2005)
A Comparison of Random Field Theory and Permutation Methods for the Statistical Analysis of MEG data
Neuroimage, 25(2):383-394, 2005Tadel 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 2019