data dict

Global var [scannerdata]

• Attributes of each trial: 
• [iArtifacts]: if the current trial is considered as a "bad" trial due to artifacts, ∈ (0: good trial; 1: bad)
• [iTrialType]: trial type {1,2,3,4,-1}
• [iInstructionLength]: length of the instruction period, ∈(100:1000 ms), source: presentation log 5xxx.
• [iOffIndex]: the block index number for current trials's light off in eegData02, ∈(1:191)
• [iOffOffset]: the offset index number for current trials's light off  in each block in eegData02, ∈ (1:12500)
• [iOnIndex]: the block index number for current trials's light on in eegData02, ∈(1:191)
• [iOnOffset]: the offset index number for current trials's light on  in each block in eegData02, ∈ (1:12500)
• Attributes with respect to the raw markers (markerData(1, x).trial & time)
• [lightOnTimeClean]: clean events of light on events (with double trigger events manually removed)
• [lightOnCleanIndex]: index of clean events in the originally markers -- gData.markerData(1,1).trial
• [lightOffTimeClean]: clean events of light off events (with double trigger events manually removed)
• [lightOffCleanIndex]: index of clean events in the originally markers -- gData.markerData(1,2).trial
• EEG channel working data
• [eegData02]: EEG working data. {Column 1: left&Right. Column2: up&down. Column3: info channel}
• Column3 info channel data format: [condition].[iTrialtype]  e.g. 54.1 = light off for proleft, 52.3 = light on for antileft

MEGANTI - Preprocessing

[Presentation sce file]
In total 14 blocks, each block has 80 trials, each trial has following four events recorded in the log file:

1. [Start]: duration 1000 ms, code 0, port_code 1
2. [Pro] or [Anti] initiation: LightOn, (green pro, red anti) duration 100 ms, code 54, port_code 54, 
3. [pro5xxx] or [anti5xxx]: randomized length, code: 5+ [100:50:1000], e.g. 5100, 5250..., port_code [101:1:117]
4. [GO cue ∈ 1 | 2 | 3 | 4] :  duration 20 ms, LightOff

• 1: greyboxproleft, port_code 201 -- prostim left
• 2 :greyboxproright, port_code 202  -- prostim right
• 3: greyboxantileft, port_code 203 -- antistim left
• 4: greyboxantiright, port_code 204 - -- antistim right

Therefore(in preprocessing_subject.m), the duration of instruction (green or red box) = 100 ms (initiation) + x ms (x is indicated by event2 in matlab code).  The actual difference between light on and off is around 117-119 ms with some trials had more than 135 ms lag (var: timeLag).


Subjects
SW - [2010-08-11] - Old system no parallel code
raw: S02_MEG54_VEF_02.ds
stim log (raw): sw32-110810-SO2-Pro+Anti-saccade task.log
Problems in the data:

1. The stim log has 195 missing event condition, all replaced with -1.
2. The lightOn marker has 130 extra double triggers - fixed (lightOnTimeClean:1121)
3. The lightOff marker has 3 extra  double triggers - fixed (lightOffTimeClean:1120)
4. Verify by comparing the time diff between on and off with the event code, 121.40 

re: Thesis Overview

TASK RELATED NEUROMAGNETIC ACTIVITY UNDERLYING THE VISUAL PERCEPTION OF VELOCITY CHANGE: A MEG STUDY

Supervisor: Dr. JFX DeSouza (link)
MEG Analyses Mentor: Dr. P Ferrari


Research questions

Part 1: Motion perception (fast & slow moving dots)

• Is there different cortical representation for fast & slow motion?
• Are there different temporal dynamics for fast & slow motion?

Part 2: Decision-making

• Subjects need to detect a change in the motion velocity and respond with button press
• When and where in the brain is a visual perception (velocity change) transformed into the neural signals for action?

Experiment

• Prior to the imaging sessions, I conducted a perceptual thresholds test (N=22) to acquire the minimal detectable increase and decrease in motion velocity for the subjects
• I set up the experimental environment and collected MEG & MRI data (N=12) with the helps from S. Bells and M. Lalancette at Toronto Sickkids hospital.
• Velocity change in the experiment was set according to each subject's perceptual thresholds, so the correct and incorrect responses could be compared
• A delayed motor response paradigm was used to separate decision-making signals from motor related signals.

Analyses

Results

Part 1 - Motion Perception

No difference in the MT+ locations (Talairach) for fast and slow motion was found (Hotelling's T2 for two multivariate independent samples)

Fig - MT+ locations
Fig - comparing the MT+ locations with previous studies

No temporal dynamics for source peak amplitude and latency found

• Velocity and visual display had no effects (3-way ANOVA)
• The amplitude and latency btw the three ROIs were different (P<.05)
• Multiple-comparison showed cuneus had higher amplitude & earlier latency than V3A & MT+

 

Part 2 - Decision-making

Comparing the grand average event-related beamformer images: 

• In the correct responses, the frontoparietal sources were observed at various time points after the velocity change onset (left column, perm-test, P<.05)
• No significant frontoparietal activations were observed in the incorrect responses (right column)

Comparing the time-frequency plots for correct and incorrect responses from IPL and SMC sources:

• IPL source showed a beta power difference between correct and incorrect responses from 200 - 400 ms (area encircled in dotted line)
• The initiation of IPL beta ERS was aligned with the high beta ERD increase in SMC after 400 ms (dotted line)

[Thesis Download]

MT+ location

Left MT+

 

 Right MT+

Problem: # 12 subject

sub#12 has noisy sensor data, but the beamformer reported good MT activation.

 

（-30    -68    1）

(-35    -66    -3)

Other subjects' RMS can be found here

Scatter plot: outlier sub#12 is in the black box

When sub#12 is excluded :

Individual virtual sensor time course at MT+, please look at sub#12:

Left Fast

Left Slow

 

 

Right Fast

 Right Slow

 

Cuneus 

Left Fast

 

 Left Slow

 

Right Fast

 

Right Fast

Current

D:\MEG\joe\backup\MEG_progs\matlab_backup\matlab2\meg_utils\topoplot

Glassbrain movies

[A001] Aligned to [motion stimulus] onset

All movies are made with neurological orientation in Tal coordinates from onset (0 ms) of visual stim to 500 ms after onset.

AB

Left_Fast

Left_Slow

Right_Fast

Right_Slow

AK

Left_Fast

Left_Slow

Right_Fast

Right_Slow

CM

Left_Fast: weak MT+

Left_Slow

Right_Fast

Right_Slow

DA

Left_Fast: interesting, contraL cuneus -> contraL V3A -> ipsiL MT+ -> contraL MT+

Left_Slow

Right_Fast

Right_Slow

ES

Left_Fast

Left_Slow

Right_Fast

Right_Slow

JD

Left_Fast:contraL MT+ then moved to ipsiL MT+

Left_Slow

Right_Fast

Right_Slow

PD

Left_Fast: V3A prior to V1 activation

Left_Slow

Right_Fast

Right_Slow

SL

Left_Fast :

Left_Slow

Right_Fast

Right_Slow

ST (this subject had no strong V3A activation)

Left_Fast

Left_Slow

Right_Fast

Right_Slow

SW

Left_Fast

Left_Slow

Right_Fast

Right_Slow

SX

Left_Fast

Left_Slow

Right_Fast

Right_Slow

WW

Left_Fast: V3A prior to cuneus

Left_Slow

Right_Fast

Right_Slow

[B002] Group avg for velocity change onset

Correct response

Incorrect response

[A002] Group avg for GO cue onset

Correct response

Incorrect response

[C] Group avg for button press

Correct response

Incorrect response

Individual RMS plots for 9 out of the total 12 subjects

Bandpass: 1-30Hz
Motion stim onset: 0 s

In each subject, the first plot is left visual display and second plot is for right. 

Subject: AB

Subject: AK

Subject: CM

 Subject: DA

 Subject: ES

Subject: JD

Subject: PD

Subject: SW 

Subject: SX

There are two markers for the visual stim: (1) one is synchronized with the onset of the motion stim, (2) The second is synched with the onset of the velocity change, which is not shown here.

MT+ ave, RMS

/Users/joseph/data/data/2_scripts/
05_makeAveRMS.txt

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