Context

This experiment, examines motor planning and control. MEG data is recorded while subjects move a cursor on screen with help of a joystick. Various motion parameters are manipulated on screen so as to examine the dynamics of motor control.

Technology

This experiment uses

MEG (306 sensors)
eye tracking (x,y position)
joystick 2D position (x,y position)

Pipeline

MEG and eye tracker data are merged "out of the box". The raw input is thus a .fif file with 308 data channels (306 MEG + x & y eye position).

The joystick data is inserted. Evoked fields are computed by condition. An anatomical MRI is used to model sources using minimum norm estimate in Brainstorm. Time-frequency source estimates are computed in FieldTrip (using DICS). ANOVAs are used to highlight ROIs. Connectivity between ROIs is estimated with imaginary coherence. Statistical inference is drawn using MEGanova.

Preprocessing

	Operation	Input format	Software	Output format	Comment / Link
1	Merge joystick and MEG	.fif	dataHandler -merge	.fif	data with MEG, eye tracker, joystick. Datahandler
2	Maxfilter	.fif	maxfilter	.fif	maxfilter
3	Detect saccades	.fif	FieldTrip	.fif	Ask script to Former user (Deleted)
4	Mark bad data segments	.fif	Muse	.fif	Review data with Muse
5	Manipulate markers to create conditions	.fif	dataHandler -adm	.fif	Creating conditions with dataHandler
6	Run ICA and reject blink and cardiac components	.fif	FieldTrip and custom script	.fif	Blink and cardiac artifact scripts
7	Create Evoked fields	.fif	dataHandler -sync -rbp	.fif	Using dataHandler to create ERFs

	Operation	Input format	Software	Output format	Comment / Link
1	Segment T1 MRI	.dic or other	recon-all (Freesurfer)	freesurfer folder	Segment MRI with Freesurfer
2	Import MEG and structural in Brainstorm	Brainstorm supported types	Brainstorm	Brainstorm internal	Data import in Brainstorm
3	Minimum norm estimate	Brainstorm internal	Brainstorm	Brainstorm internal	See tutorials 20 and following of the Brainstorm tutorials
4	Project sources on template	Brainstorm internal	Brainstorm	Brainstorm internal	See tutorial on Brainstorm website
5	Temporal averages	Brainstorm internal	Brainstorm?	Brainstorm internal?	ask Former user (Deleted) how he did it
6	ROI design with statistics	Brainstorm internal	MegAnova	Brainstorm internal	Using statistics to define ROIs in Brainstorm
7

FieldTrip source space time-frequency analysis

	Operation	Input format	Software	Output format	Comment / Link
1	Import fif into FieldTrip	.fif	FieldTrip	FieldTrip .mat	Import .fif into FieldTrip
2	Run DICS source reconstruction	(any)	FieldTrip	FieldTrip .mat	Localizing oscillatory sources using beamformer techniques
3	Run ANOVAs on TF windows of interest	FieldTrip .mat	MegAnova	???	Using Meganova to run ANOVAs
4	Compute ROI imaginary coherence	FieldTrip .mat	FieldTrip	FieldTrip.mat	Causality analysis in FieldTrip

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http://www.fieldtriptoolbox.org/tutorial/beamformer

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