MT+ localization

A001_FastSlow_GetRawData(1, aSubjects, [1 1 1 1], 1, 4, 7)
A001_FastSlow_GetRawData(1, aSubjects, [1 1 1 1], 1, 8, 12)
A001_FastSlow_GetRawData(1, aSubjects, [1 1 1 1], 1, 15, 30)
A001_FastSlow_GetRawData(1, aSubjects, [1 1 1 1], 1, 30, 60)




April 24
A01_FastSlow_assembleRawData()
New function for read data from .mat file and assemble matrix for analysis.
  aSubjects = {'AB', 'AK', 'CM', 'DA', 'ES', 'JD', 'PD', 'SL', 'ST', 'SW','SX', 'WW'};
A001_FastSlow_assembleRawData(1, aSubjects)

April 23
New function readTrialsFromRaw()
Added external RMS function: rms.m

Motion localizer figs:
/Users/joseph/data/data/7_SPM2/05_MT_localization/jpg/



function A001_FastSlow_GetRawData(onJoeServer, aSubjects, toDo, doBeamformer)
New function for searching peaks in ctf and do beamformer


aSubjects = {'AB', 'AK', 'CM', 'DA', 'ES', 'JD', 'PD', 'SL', 'ST', 'SW', 'SX', 'WW'};
 A001_FastSlow_GetRawData(1, aSubjects, [1 1 1 1], 1)


function A001_FastSlow_MT(aSubjects, toDo, dataHome)
New function for permutation and calculate glass brain for three regions:
primary visual (V1), V3A,and MT+

output:
/Users/joseph/data/data/7_SPM2/04_permutation/A001_MT/

aSubjects = {'AB', 'AK', 'CM', 'DA', 'ES', 'JD', 'PD', 'SL', 'ST', 'SW', 'SX', 'WW'};
A001_FastSlow_MT(aSubjects, [1 0 0 0])
A001_FastSlow_MT(aSubjects, [0 0 1 0])
A001_FastSlow_MT(aSubjects, [0 0 0 1])
A001_FastSlow_MT(aSubjects, [0 1 0 0])

A001 Stimulus onset - Left, right, fast, slow -- collapsed

2010/03/04

(1)Create $Datahome/02_script/03_A001_Combined_ERB_2.5cm run beamformers
IMPORTANT CHANGE!
In dataset that is aligned to the onset of stimulus, there are two folders:
ANALYSIS_A001: stimulus onset
ANALYSIS_A002: velocity onset

(2)normalization for the ERB (A001 correct and err), in matlab run:
Combo_A001_Correct_normlization
Combo_A001_Err_normlization

(3) scripts for ERB permutation
New function, changed the parameters, plot_permutation_tfr_sheng_v2.m


Combo_A001_permute_batch(1,50)  % start time, end time, unit 10 ms for correct and error permunation


!!! Check log file after running !!!

(4) permutation threshold, plotting glass brains
    D:\MEG\joe\data\7_SPM2\02_averaging\A001_Correct (local)
       Saved threshold and max scale in 
       tCorrectA001.xls ==> tCorrectA001.mat
       Server: /Users/joseph/data/data/7_SPM2/02_averaging/A001_Correct/

    D:\MEG\joe\data\7_SPM2\02_averaging\A001_Err  
       tErrA001.xls ==> tErrA001.mat  
       Server: /Users/joseph/data/data/7_SPM2/02_averaging/A001_Err/

  Combo_A001_Correct_glassBrain(1, 50, 1, 1)
  Combo_A001_Err_glassBrain(1, 50, 1, 1)

MT+

Gitelman, D. R., A. C. Nobre, et al. (1999). "A large-scale distributed network for covert spatial attention." Brain 122(6): 1093-1106.
 

Fig. 6 Foci of activations in the temporo-occipital region. Filled circles (d) denote the locations found in the current study. The foci of activations in MT (E, G, C) and an area subserving movement-related knowledge (e) are taken from several previous studies (Zeki et al., 1991; Martin et al., 1995; Beauchamp et al., 1997; Dupont et al., 1997; Chawla et al., 1998).





 Spatiotemporal Activity of a Cortical Network for Processing VisualMotion Revealed by MEG and fMRIAHLFORS

Clarification of the events and baseline

Four events of interest and baseline windows

TFR data

http://dl.dropbox.com/u/14828654/motionMEG/doc/manuscript/figs.xls
http://dl.dropbox.com/u/14828654/motionMEG/doc/manuscript/ROI_memo_combo.xls
http://dl.dropbox.com/u/14828654/motionMEG/doc/manuscript/ROI_TFR_compare.xls
http://dl.dropbox.com/u/14828654/motionMEG/doc/manuscript/ROI_TFR.xls

Download ROIs TFR figs （Updated 2011-01-04）

L_ACC/medial frontal G.

Cohen, M. X., K. R. Ridderinkhof, et al. (2008). "Medial frontal cortex and response conflict: Evidence from human intracranial EEG and medial frontal cortex lesion." Brain Research 1238: 127-142.

stimulus on at 0 s, GO cue at 2.2 s,

speed change onset at somewhere around 1 s

key pressed at 0 s

Peri-response, we also observed enhancements in lower band power(delta) following the desynchronization in the beta band. The pre-response beta and post-response theta changes look related to each other -- need to statistically verify this.

L_SMC

Beta oscillation suppressions around motor and supplementary motor regions have been linked to motor preparatory processes (Miller et al., 2007; Neuper et al., 2006; Pfurtscheller et al., 2003) and are thought to reflect decreased global neural coherence during the processing and planning of movements. 

L_SMC

Beta band power difference in preCun pre-stimulu

Free surfer notes

http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide

Basics neuronal dynamics

Climesh review on bands (2008)

Delta 0-1 Hz: neocortical, and thalamo-cortical networks.  Large-scale cortical integration.

Theta: subcortical and thalamo-cortical source, involved in a variety of cognitive functions (Hipo theta).

Alpha 8 - 13 Hz: amplitude is related to the level of cortical activation, strong alpha associated with coritcal & behavioural deactivation or inhibition; otherwise (1) highly specific perceptual, attentional, and memory processes.

Beta:
cortically generated (Gross 2004 reported a large scale beta too), b/c of local strictness.  Mainly associated with motor, ERD before/during movement, rebound after the movement stopped.
Attention and higher cognitive functions.

Gamma:
cortically generated too (from intrinsic membrane properties of interneurons or from neocortical exitatory-inhibitory circuits)
* binding
* more recent --> human gamma frequency were reported for encoding, retention and retrieval of info independent of sensory modality.
Problem: small amplitude, similarity to muscle activity leaks into the sensors.



During cognitive efforts: * delta, theta, gamma ERS (pp. 3)
During cognitive processing: * alpha, beta ERD



Super-fast processes (a few ms level), i.e. Buzsaki and Draguhn, 2004; Dragoi and Buzsaki, 2006; Siapas et al., 2005



Varela et al., 2001 review on Phase synchronization


Phase synchronization

(1) Phase coupling over distance (phase-coherence)
(Nunez et al., 1997, 1999; or Rappelsberger, 1998)

• pp 5, widespread coherence in gamma& alpha bands in conscious perception vs unpercepted stim (Rodriguez et al., 1999; Klopp et al., 2000; Mima et al., 2001).
• pp 7,  (Sauseng et al., 2007a) midline theta, increased with task-demand (power diff independent of novelty), in line with literature on sustained attention, localized into ACC, cingulate motor area.   But long range fronto-parietal theta phase coherence was stronger in the novel condition.

(2) Phase synchronization acrossing different frequency (bi-coherence)

• Network of diff size are supposed to oscillate at diff speed
• High temporal preciseness of synch btw oscillations of diff freq can potentially explain how info btw mem sys can be exchanged in cortex。

• instantaneous phase of a slower oscillation modulates the amplitude of a higher freq (Lakatos et al., 2005). delta --> theta, theta --> gamma, hierarchical organization.
• in humans, theta --> gamma (Mormann et al., 2005; Demiralp et al., 2007a,b; Canolty et al., 2006).
• theta --> alpha interact in combined working and long-term memo (Sauseng et al., 2002, theta from anterior to posterior during memo retrieval attempts. When visual items retrieved, the direction of theta reversed. At this theta reversal, upper alpha power decrease -- indicating successful retrieval)
• Methods: Cross-freq phase synchronization (bi-coherence) - Schack: momory-load dependent increase of pase coupling btw prefrontal theta and posterior alpha.  Interpretation: prefrontal theta -> executive processes of working-memo, posterior alpha --> reactivated long-term memo traces (Ruchkin 2003) - thus, working and long-term memo interfacing (Schack 2005)
• Sauseng (2008) theta-gamma coherence in pareital modulated by short-term memory load

(3) Phase-locking after stim presentation

• Look up: 
• Basar, E., 1999a. Brain Function and Oscillations I: Principles and Approaches. Springer, Berlin.
• Basar, E., 1999b. Brain Functions and Oscillations, II: Integrative Brain Functions.Springer, Berlin.
  

• pp 9, there are still ongoing debates over phase resetting or the classical evoked model, and Sauseng (2007b) these two cannot be dessociated <-- should take a look at this paper
• Pase-locking index, Gruber 2005, Schack & Klimesch 2002
  

Event-related changes

Journal club presentation 1

Pfurtscheller Handbook page 7
(1) Evoked response: time-locked & Phase-locked, which could be found from simple averaging. It's the response of a stationary system to the external stimulus.
(2) Induced response: time-locked but NOT phase-locked, can only be extracted through non-linear methods (e.g. envelope detection or power spectral analysis). It could be understood as a change in the ongoing activity, resulting from the changes in the functional connectivity within the cortex.Various factors: may depend on modulating influence arising from neurochemical brain systems, on changes in the strength of synaptic interactions or on changes affecting the intrinsic membrane properties of local neurons.

functional meaning, Pfurtcheller handbook chapter 
Pfurtscheller's ERD during visual processing
Pfurtscheller's basic principles on ERD/ERS ◄═ important paper









Thomas F. Collura 
President of the International Society for Neurofeedback and Research (ISNR).
lecture： Foundations of Neuronal Dynamics & Z Scores 

100ms perception
200ms awareness
300ms differentiate
400ms detection

signal 60-70 ms reaches thalamus, then 100 to occipital, visual alpha: 10 Hz when resting or there is no visual stimulus

delta: 1-4 Hz

Theta: 4-7 Hz

alpha: 7 -15 Hz
high alpha or low beta SMR in SMC: 14 Hz, a very healthy, vigilant state, no body movement (physical relaxation), in SMC typical thalamo-cortical speed is 80 ms in resting, faster than the visual system.  (part 11 in the talk)

beta: 15 - 20 Hz more localized (memory recall), wax and wane, sinusoidal

high beta: 20 - 30 ms, thinking, intensive thinking, worrying, math, wax and waning

gamma: 40 Hz and above
*indicate sensory binding, perceptual binding (association)  high gamma synchrony in meditation experts, and clairvoyant subjects.  R. Davidson lab. 
* Gamma nested in theta

Lenox