Differences between revisions 2 and 50 (spanning 48 versions)

Biomag 2016 satellite meeting

From raw MEG to publication:
How to perform MEG group analysis with free academic software.

General information

When	October 2nd, 8:30-1pm
Where	TBA
Speakers	Alexandre Gramfort	MNE, Telecom ParisTech
	Vladimir Litvak Rebecca Beresford	SPM, UCL, UK
	Leighton Hinkley	NUTMEG, UCSF, USA
	Robert Oostenveld	FieldTrip, Donders Inst., The Netherlands
	Francois Tadel	Brainstorm, McGill Univ., Canada
Registration	40$ \| 71 registered participants
Links	Satellite meeting page \| Conference website

Online resources

Abstract

Free academic toolboxes have gained increasing prominence in MEG analysis as a means to disseminate cutting edge methods, share best practices between different research groups and pool resources for developing essential tools for the MEG community. In the recent years large and vibrant research communities have emerged around several of these toolboxes. Teaching events are regularly held around the world where the basics of each toolbox are explained by its respective developers and experienced power users. There are, however, two knowledge gaps that our BIOMAG satellite symposium aims to address. Firstly, most teaching examples only show analysis of a single ‘typical best’ subject whereas most real MEG studies involve analysis of group data. It is then left to the researchers in the field to figure out for themselves how to make the transition and obtain significant group results. Secondly, we are not familiar with any examples of fully analyzing the same group dataset with different academic toolboxes to assess the degree of agreement in scientific conclusions and compare strengths and weaknesses of various analysis methods and their independent implementations. Our workshop is organised by the lead developers of six most popular free academic MEG toolboxes (in alphabetic order): Brainstorm, EEGLAB, FieldTrip, MNE, NUTMEG, and SPM. Ahead of the workshop the research team for each toolbox will analyze the same group MEG/EEG dataset. This dataset containing evoked responses to face stimuli was acquired by Richard Henson and Daniel Wakeman, who won a special award at BIOMAG2010 to make it freely available to the community. All the raw data are available at https://openfmri.org/dataset/ds000117/.

Detailed instructions for each toolbox will be made available online including analysis scripts and figures of results. All analyses will show a full pipeline from the raw data to detailed publication quality results. Researchers who are interested in using the respective toolbox will then be able to reproduce the analysis in their lab and port it to their own data.

At the workshop each group will briefly introduce their software and present the key results from their analysis. This will be followed by a panel discussion and questions from the audience.

Following the event we plan to integrate the suggestions and questions from the workshop audience and to publish the analyses details as part of a special research topic in Frontiers in Neuroscience, section Brain Imaging Methods so that the proposed best practices will be endorsed by peer review and become citable in future publications. Other research groups will be invited to contribute to the research topic as long as they present detailed descriptions of analyses of group data that are freely available online and make it possible for others to fully reproduce their analysis and results.

We hope that this proposal will lead to creation of invaluable resource for the whole MEG community and the workshop will contribute to establishment of good practice and promoting consistent and reproducible analyses approaches. The event will also showcase all the toolboxes and will be of interest to beginners in the field with basic background in MEG who contemplate the most suitable analysis approach and software for their study as well as to experienced researchers who would like to get up to date with the latest methodological developments.

Program

Each group will present their software and develop more specifically one topic common to all the programs.

Introduction	Presentation of the dataset
Brainstorm	Single subject tutorial Group analysis tutorial Slides: powerpoint \| pdf
FieldTrip	http://www.fieldtriptoolbox.org/workshop/biomag2016
MNE	http://mne-tools.github.io/mne-biomag-group-demo/
NUTMEG	www.nitrc.org/plugins/mwiki/index.php/nutmeg:MainPage

8:30-9:00	Welcome and registration
9:00-9:15	Introduction to the dataset
9:15-9:45	FieldTrip, Robert Oostenveld Highlight: Reading and converting files with the fileio library
9:45-10:15	MNE, Alexandre Gramfort Highlight: Pre-processing and filtering
10:15-10:45	Brainstorm, Francois Tadel Highlight: Data reviewing, event marking and epoching
10:45-11:00	Coffee break
11:00-11:30	NUTMEG, Leighton Hinkley Highlight: Time-frequency analysis
11:30-12:00	SPM, Rebecca Beresford & Vladimir Litvak Highlight: Averaging/Combine planar
12:10-13:00	Panel discussion Moderator: Jason Taylor, Univ Manchester, UK

SPMSPM12 Manual, chapter 42

Slides: Rebecca Beresford | Vladimir Litvak

Contact

For registration questions, please contact: biomag2016@biomag2016.org

For questions regarding the program, please contact Vladimir Litvak ( v.litvak@ucl.ac.uk ) or Francois Tadel ( francois.tadel@mcgil.ca ).

-  ⇤ ← Revision 2 as of 2016-09-14 16:21:46 → 
  Size: 5887
  Editor: FrancoisTadel
  Comment:
+   ← Revision 50 as of 2016-10-08 13:33:22 → ⇥
  Size: 7894
  Editor: FrancoisTadel
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 2:
-From raw MEG to publication: How to perform MEG group analysis with free academic software
+''From raw MEG to publication: <<BR>>How to perform MEG group analysis with free academic software.''
 Line 7:
-<<HTML(<TR><TD>)>>'''Date'''<<HTML(</TD><TD>)>>October 2nd, 8:30-1pm <<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>October 2nd, 8:30-1pm <<HTML(</TD></TR>)>>
 Line 9:
-<<HTML(<TR><TD>)>>'''Organizers'''<<HTML(</TD><TD>)>>Arnaud Delorme (EEGLAB, UCSD)<<BR>>Alexandre Gramfort (MNE-Python, Telecom ParisTech)<<BR>>Vladimir Litvak (SPM, UCL)<<BR>>Srikantan Nagarajan (NUTMEG, UCSF)<<BR>>Robert Oostenveld (FieldTrip, Donders Institute)<<BR>>Francois Tadel (Brainstorm, McGill) <<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>>TBA <<HTML(</TD></TR>)>>
 Line 11:
-<<HTML(<TR><TD>)>>'''Registration'''<<HTML(</TD><TD>)>>Registration to this workshop is handled on the conference website.<<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>'''Speakers'''<<HTML(</TD><TD>)>>Alexandre Gramfort<<HTML(</TD><TD>)>>'''MNE''', Telecom ParisTech<<HTML(</TD></TR>)>>
 Line 13:
-<<HTML(<TR><TD>)>>'''Links'''<<HTML(</TD><TD>)>>[[http://www.biomag2016.org/satellite_meetings2.php|Satellite meeting page]] | [[http://www.biomag2016.org/|Conference registration]]<<HTML(</TD></TR>)>>
+<<HTML(<TR><TD></TD><TD>)>>Vladimir Litvak<<BR>>Rebecca Beresford<<HTML(</TD><TD>)>>'''SPM''', UCL, UK<<HTML(</TD></TR>)>>

<<HTML(<TR><TD></TD><TD>)>>Leighton Hinkley<<HTML(</TD><TD>)>>'''NUTMEG''', UCSF, USA<<HTML(</TD></TR>)>>

<<HTML(<TR><TD></TD><TD>)>>Robert Oostenveld<<HTML(</TD><TD>)>>'''FieldTrip''', Donders Inst.,  The Netherlands<<HTML(</TD></TR>)>>

<<HTML(<TR><TD></TD><TD>)>>Francois Tadel<<HTML(</TD><TD>)>>'''Brainstorm''', McGill Univ., Canada<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Registration'''<<HTML(</TD><TD colspan=2>)>>40$ | 71 registered participants<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Links'''<<HTML(</TD><TD colspan=2>)>>[[http://www.biomag2016.org/satellite_meetings2.php|Satellite meeting page]] | [[http://www.biomag2016.org|Conference website]]<<HTML(</TD></TR>)>>
-Line 16:
+Line 26:
+== Online resources ==
<<HTML(<TABLE>)>>

<<HTML(<TR><TD>)>>'''Introduction'''<<HTML(</TD><TD>)>>[[ftp://neuroimage.usc.edu/pub/doc/MultiModalDataset.pptx|Presentation of the dataset]] <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Brainstorm'''<<HTML(</TD><TD>)>>[[Tutorials/VisualSingle|Single subject tutorial]]

[[Tutorials/VisualGroup|Group analysis tutorial]]

Slides: [[ftp://neuroimage.usc.edu/pub/doc/biomag2016_brainstorm.pptx|powerpoint]] | [[ftp://neuroimage.usc.edu/pub/doc/biomag2016_brainstorm.pdf|pdf]] <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''FieldTrip'''<<HTML(</TD><TD>)>>http://www.fieldtriptoolbox.org/workshop/biomag2016

<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''MNE'''<<HTML(</TD><TD>)>>http://mne-tools.github.io/mne-biomag-group-demo/

<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''NUTMEG'''<<HTML(</TD><TD>)>>www.nitrc.org/plugins/mwiki/index.php/nutmeg:MainPage <<HTML(</TD></TR>)>>
-Line 29:
+Line 60:
+Each group will present their software and develop more specifically one topic common to all the programs.
-Line 31:
+Line 64:
-<<HTML(<TR><TD>)>>8:30-9:00<<HTML(</TD><TD>)>>Welcome  <<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>8:30-9:00<<HTML(</TD><TD>)>>Welcome and registration <<HTML(</TD></TR>)>>
-Line 33:
+Line 66:
-<<HTML(<TR><TD>)>>9:00-10:00<<HTML(</TD><TD>)>>'''Lecture: Brainstorm overview (Tadel)'''
+<<HTML(<TR><TD>)>>9:00-9:15<<HTML(</TD><TD>)>>Introduction to the dataset <<HTML(</TD></TR>)>>
-Line 35:
+Line 68:
-Software structure, typical data workflow <<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>9:15-9:45<<HTML(</TD><TD>)>>'''FieldTrip''', Robert Oostenveld
-Line 37:
+Line 70:
-<<HTML(<TR><TD>)>>10:00-10:45<<HTML(</TD><TD>)>>'''Practice'''
+<<HTML(<FONT color=#BBBBBB>)>>Highlight: Reading and converting files with the fileio library<<HTML(</FONT></TD></TR>)>>
-Line 39:
+Line 72:
-Database explorer
+<<HTML(<TR><TD>)>>9:45-10:15<<HTML(</TD><TD>)>>'''MNE''', Alexandre Gramfort
-Line 41:
+Line 74:
-MRI volumes, surfaces and anatomical atlases<<HTML(</TD></TR>)>>
+<<HTML(<FONT color=#BBBBBB>)>>Highlight: Pre-processing and filtering<<HTML(</FONT></TD></TR>)>>

<<HTML(<TR><TD>)>>10:15-10:45<<HTML(</TD><TD>)>>'''Brainstorm''', Francois Tadel

<<HTML(<FONT color=#BBBBBB>)>>Highlight: Data reviewing, event marking and epoching <<HTML(</FONT></TD></TR>)>>
-Line 45:
+Line 82:
-<<HTML(<TR><TD>)>>11:00-12:30<<HTML(</TD><TD>)>>'''Practice'''
+<<HTML(<TR><TD>)>>11:00-11:30<<HTML(</TD><TD>)>>'''NUTMEG''', Leighton Hinkley
-Line 47:
+Line 84:
-Registration EEG/MRI
+<<HTML(<FONT color=#BBBBBB>)>>Highlight: Time-frequency analysis<<HTML(</FONT></TD></TR>)>>
-Line 49:
+Line 86:
-Review of continuous EEG recordings
+<<HTML(<TR><TD>)>>11:30-12:00<<HTML(</TD><TD>)>>'''SPM''', Rebecca Beresford & Vladimir Litvak
-Line 51:
+Line 88:
-Montage editor and management of event markers
+<<HTML(<FONT color=#BBBBBB>)>>Highlight: Averaging/Combine planar<<HTML(</FONT></TD></TR>)>>
-Line 53:
+Line 90:
-Frequency filters<<HTML(</TD></TR>)>>
+<<HTML(<TR><TD>)>>12:10-13:00<<HTML(</TD><TD>)>>'''Panel discussion'''
-Line 55:
+Line 92:
-<<HTML(<TR><TD>)>>12:30-13:30<<HTML(</TD><TD>)>>''Lunch''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>13:30-15:30<<HTML(</TD><TD>)>>'''Practice'''

Bad channels management

Artifact  detection

Artifact correction with SSP and ICA

Averaging, exploring the evoked response<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>15:30-16:00<<HTML(</TD><TD>)>>''Coffee break''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>16:00-16:30<<HTML(</TD><TD>)>>'''Lecture: Source modeling (Baillet)'''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>16:30-17:30<<HTML(</TD><TD>)>>'''Practice'''

Head modeling, cortical source reconstruction

Regions of interest (ROIs) <<HTML(</TD></TR>)>>
+Moderator: Jason Taylor, Univ Manchester, UK <<HTML(</TD></TR>)>>
-Line 79:
+Line 96:
-== Resource ==
+<<HTML(<TR><TD>)>>'''SPM'''<<HTML(</TD><TD>)>>[[http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf#Chap:data:multi|SPM12 Manual, chapter 42]]

Slides: [[ftp://neuroimage.usc.edu/pub/doc/BioMag2016_Beresford_Oct2016.ppt|Rebecca Beresford]] | [[ftp://neuroimage.usc.edu/pub/doc/V_Litvak_SPM_preprocessing.pptx|Vladimir Litvak]] <<HTML(</TD></TR>)>>

<<HTML(</TABLE>)>>

== Contact ==
For registration questions, please contact: biomag2016@biomag2016.org

For questions regarding the program, please contact Vladimir Litvak ( v.litvak@ucl.ac.uk ) or Francois Tadel ( francois.tadel@mcgil.ca ).

Software

Users

Development