Sunday, January 9, 2011

re: HBM abstract


Abstract Final [Download]
TFR figs [Download]
A overview of all the ROIs' TFR: [Download]
2010 Frontal lobe poster:  [Download]

http://dl.dropbox.com/u/14828654/motionMEG/doc/201106_HBMO/ROI_TFR_compare.xls
http://dl.dropbox.com/u/14828654/motionMEG/doc/201106_HBMO/ROI_TFR.xls







I am planning to report the underlined results in the abstract, and currently looking up literature for explanation to the data.

Event A:
  • fronto-parietal region had higher prestimulus alpha band power for correct trials.
  • L_PM_BA9 showed less power change in lower band and beta band.

Support:
[1] Min & Herrmann (2007) tasks required the inhibition of the task-irrelevant feature. Found significantly higher prestimulus total alpha activity (at Pz) in the shape task than the color task. ==> top-down processing prior to stimulation would be reflected in the prestimulus ongoing alpha activity.
[2] Min (2008)  found significantly higher prestimulus alpha activity ==> constant inter-trial interval condition yielded significantly shorter reaction times than variable interval ==> indicating more efficient preparation for upcoming stimuli during the constant ISI.

But, Ergenoglu (2004) and Hanslmayr(2007) found opposite result, higher alpha power in non-perceiver in Pz, Oz.






Event B:
  • left premotor BA9 and IPL both had higher high-beta band synchronization (0 - 0.2 s) in error trials. 
  • L_IPL and L_SMC both showed a higher alpha synchronization around 0.3 - 0.4s in the error trials
  • possibly the left insula played a role here too.
  • Error trials had more alpha power increase in the fronto-parietal region after the speed change.  

Event A002: 
  • correct trials had higher low-band (delta&theta) power increase and more beta desychronization in left SMC before and after the GO cue.

Event C:
  • more alpha band power increase prior to the key onset in error trials. Left IFG gamma band showed interesting pattern, but did not have a very good statistical result.

-- I feel the abstract might look a little too busy if I include everything underlined above, what do you think?








Min, B.-K. and C. S. Herrmann (2007). "Prestimulus EEG alpha activity reflects prestimulus top-down processing." Neuroscience letters 422(2): 131-135.
    In order to test the hypothesis that prestimulus alpha activity reflects top-down inhibitory processing, EEG was recorded from 16 subjects performing a color and a shape discrimination task. Both tasks required the inhibition of the task-irrelevant feature. Longer reaction times and P3 latencies showed that the shape task was more difficult than the color task. We suppose that these different task-difficulties are due to a higher salience of the color feature as compared to the shape feature. Interestingly, we observed significantly higher prestimulus total alpha activity in the shape task than the color task. We concluded that the inhibition of the more salient color feature in the shape task resulted in enhanced prestimulus alpha activity. Such a relationship between prestimulus alpha and poststimulus performance implies that prestimulus alpha reflects prestimulus top-down processing for preparing subsequent task-performance. Since we observed the [`]task' effect of prestimulus alpha activity also in reaction times and in P3 latencies, prestimulus alpha seems to predict such poststimulus responses. Consequently, prestimulus ongoing alpha activity probably reflects top-down information and modulates subsequent poststimulus responses.

Min, B.-K., J. Y. Park, et al. (2008). "Prestimulus EEG alpha activity reflects temporal expectancy." Neuroscience letters 438(3): 270-274.
    Since prestimulus EEG alpha activity has recently been considered to convey prestimulus top-down processing, we investigated whether prestimulus alpha activity reflects temporal expectancy of upcoming stimulation even under the non-classical contingent negative variation (CNV) paradigm. EEG was recorded from 16 subjects performing a color and a shape discrimination task manipulated with constant and variable inter-stimulus interval (ISI) conditions. The power of oscillatory activity was investigated by convolving the EEG signals with Morlet wavelets. The constant ISI condition yielded significantly shorter reaction times than the variable ISI condition, indicating more efficient preparation for upcoming stimuli during the constant ISI. We found significantly higher prestimulus alpha activity in the constant ISI condition than in the variable ISI condition, but no significant CNV even in the constant ISI condition. Such a reflection of temporal expectancy in the prestimulus alpha activity corroborates that the prestimulus top-down mental state for preparing upcoming task-performance is considerably reflected in the prestimulus ongoing alpha activity.









Ergenoglu, T., T. Demiralp, et al. (2004). "Alpha rhythm of the EEG modulates visual detection performance in humans." Cognitive Brain Research 20(3): 376-383.
    The effects of the changes in the frequency spectrum of the electroencephalogram (EEG) on the perception of near-threshold visual stimuli and on the event-related potentials (ERPs) produced by these stimuli were investigated on 12 healthy volunteers. The stimulus intensity, at which each subject could detect 50% of the presented stimuli, was defined as the sensory threshold for that subject. Single ERP trials were separated into two groups: trials with detected and undetected stimuli. The ERPs and the average power spectra of the 1 s prestimulus periods were computed for both conditions. P300 amplitudes of the ERPs, and total power and relative band powers of the delta (0.5-4 Hz), theta (4-7.5 Hz), alpha (7.5-13 Hz), beta (13-30 Hz), and gamma (30-70 Hz) frequency bands of the prestimulus power spectra were measured. Between the two conditions, a specific difference was observed in the relative power of the alpha band, which was significantly lower before detected stimuli (p<0.01) in line with significantly higher amplitudes of the ERPs (p<0.001). These results show that short-lasting changes in brain's excitability state are reflected the relative alpha power of the EEG, which may explain significant variability in perceptual processes and ERP generation especially at boundary conditions such as sensory threshold.
 


Hanslmayr, S., A. Aslan, et al. (2007). "Prestimulus oscillations predict visual perception performance between and within subjects." NeuroImage 37(4): 1465-1473.
    In the present study, the electrophysiological correlates of perceiving shortly presented visual stimuli are examined. In particular, we investigated the differences in the prestimulus EEG between subjects who were able to discriminate between four shortly presented stimuli (Perceivers) and subjects who were not (Non-Perceivers). Additionally, we investigated the differences between the subjects perceived and unperceived trials. The results show that Perceivers exhibited lower prestimulus alpha power than Non-Perceivers. Analysis of the prestimulus EEG between perceived and unperceived trials revealed that the perception of a stimulus is related to low phase coupling in the alpha frequency range (8-12 Hz) and high phase coupling in the beta and gamma frequency range (20-45 Hz). Single trial analyses showed that perception performance can be predicted by phase coupling in the alpha, beta and gamma frequency range. The findings indicate that synchronous oscillations in the alpha frequency band inhibit the perception of shortly presented stimuli whereas synchrony in higher frequency ranges (> 20 Hz) enhances visual perception. We conclude that alpha, beta and gamma oscillations indicate the attentional state of a subject and thus are able to predict perception performance on a single trial basis.

 

Wednesday, December 29, 2010

HBM 2011

http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3419

Abstract submission for the 17th Annual Meeting of the Organization for Human Brain Mapping to be held in Québec City, Canada, June 26-30, 2011 is now open. The deadline to submit has been extended to January 10, 2011. Please note that this deadline is firm, there will be no further extensions.

some updates

I located the bug with some ROI's TFR permutation test (TFR data not-assigned error only for induced response, but I don't think I have time to fix it right now.  I am work on the full spectrum data for the current work, if it is necessary to look at the induced response, then I will have to fix the bug myself).

Filling in this table -- I'm working on the data full time tomorrow, should be able to finish this and assemble the figs by mid night.



Left ACC activation:
Writing some scripts to plot individual TFR for left ACC




close look at 1-40 Hz:




Right ACC
hi-gamma started from around 1 s after A onset



L_SMC


Sunday, December 26, 2010

Re: MEGANTI notes

I think it should be a good idea to use the same protocols for naming, folder structures, and especially important for the naming of Matlab scripts if we analyze different MEG projects under one server. This fig shows the steps for analysis, will show more detail when I have time.




MEG dataset are under folder:
/root/MEGANTI/data/XX
XX is each subject's initial.

Preprocessing first step: Marker files.

It is to find out the events of interest and save the timestamps of each event into text files for further epoching the datasets (for example, "Instruction", "GO_cue", etc.

Each subject's main marker file "MarkerFile.mrk" is under each subject's raw MEG dataset. e.g. subject AB's main marker file is under:
/root/MEGANTI/data/AB/S07_MEG54_VEF_02.ds/
The marker file could be open with any text editor.Please refer to Jason's notes for the meaning of the events in the MarkerFile.mrk ("LightOn", "LightOff"...) and Presentation's log files. 


I usually copy each subject's main marker file to the folder where I save Presentation's log file, e.g. /root/MEGANTI/data/00_gain/XX (XX is subject's initial, I think I only did for subject SW).  After I am done with all the event's marker, I will copy the marker files (e.g. Instruction.txt, Go_cue.txt) to /root/MEGANTI/data/XX/markers
You only need two columns in each event's marker file, first column is the trial number, the second column is the offset from where the current trial begins (this "trial" is the trial length for MEG recording = 20 s/trial, not the actual the experiment's trial length). 
e.g.
Marker file "Instruction.txt" should be something like this:
            +0            +4.273600
            +2            +3.158400
            +2            +13.193600
            +2            +17.808000
            +3            +2.544000
            +5            +2.974400
            +6            +7.227200
            +6            +16.692800
            +7            +0.710400
            +9            +2.710400
            +9            +11.494400
            +11            +12.478400
            +15            +4.347200
            +16            +19.947200
            +17            +13.998400
            +18            +3.448000
            +19            +9.979200
            ...


Second step: adding markers and epoching

All the linux scripts are saved under:
/root/MEGANTI/data/02_scripts/

After we are done with all the event's marker files for each subject, we should then copy each subject's marker files (e.g. Instruction.txt, Go_cue.txt) to /root/MEGANTI/data/XX/markers.  Next, we will need to write scripts for adding the markers to the raw dataset and epoching the data.
(a) Adding the markers:
e.g. For subjecg SW, we first log onto the Linux console with root account, then run:
export dataHome=~/MEGANTI/data
cd $dataHome/SW
export RAW_DS=S02_MEG54_VEF_02.ds
addMarker -f -n
Instructions -l red -p markers/Instructions.txt $RAW_DS
(This marker "Instructions" would now be added to the main marker file)

(b) Epoching. After adding the markers, we run newDs to generate new datasets:
newDs -f -overlap 3 -marker "Instructions"  -time -2 2.5 $RAW_DS SW_Instructions_-2.25_2.45.ds

Third step: Creating multi-sphere head models
To be continued...
Fiducial markers are under:
/root/MEGANTI/doc/fiducial/

Note:
(1) The MRI files need to be converted into CTF v2 format .mri file before we could run the headmodeling scripts
(2) The head modeling scripts must be run from Matlab GUI.
(3) Convention: the .mri file should be under each subject's home folder (/root/MEGANTI/data/XX/), the raw dataset usually are taken as the default dataset for creating head models.
e.g.  makeHeadModels('/root/MEGANTI/data/SW/SW_V2.mri', '/root/MEGANTI/data/SW/S02_MEG54_VEF_02.ds') 


Fourth step:run event-related beamformers:
To be continued...

re: matlab scripts notes

permute_vs_tfr_sheng.m logic:
modified its code and export all the data to mat files.


new function for plotting permute_tfr:
function plot_permutation_tfr_sheng(perm_matFile, freqWindow, timeWindow )

need to find bugs in getting raw files (e.g. B002 L_ST_MT_BA39)

Friday, December 17, 2010

Visual alpha -- to be continued

G.Pfurtscheller 1994 paper gives a good explanation event-related desychronization (ERD) in alpha band in the visual system. (Pfurtscheller is the person coiled term ERD)
"Two different types of ERD can be differentiated: one short-lasting, localized to occipital areas and involving upper alpha components; the other longer lasting, more widespread, most prominent over parietal areas and maximal for lower alpha components. The former most likely reflects primary visual processing and feature extraction, the latter is more related to  cognitive processing and mechanisms of attention. "

N. Yamagishi (2005) reported attentional shifts modifies the latency and the amplitude in MEG induced responses in cuneus region (BA17).
Fig. 4. Group analysis (n = 14) showing event-related spectral perturbation (ERSP) plots derived from the activation waveforms of the ICs reflecting calcarine activity for each subject and for each experimental condition (ISI = 1000 ms). The plots consist of 25 equally spaced bins with center frequencies ranging from 1.95 to 48.8 Hz and 32 equally spaced time steps with centers at 72 to 1372 ms. The group-mean ERSP plots show postcue power differences (in dB) referenced to a 200 ms precue baseline recording for (a) attention directed away from the stimulus and (b) attention directed towards the stimulus. Both spectral power increases (reddish hues) and decreases (bluish hues) are evident. A random effects one-sample t test indicating significant ( P < 0.05 FDR corrected; df = 13) positive (reddish hues) and negative (bluish hues) event-related spectral power changes are shown for (c) attention directed away from the stimulus and (d) attention directed towards the stimulus. The cue onset time (t = 0 ms) and the stimulus onset time (t = 1000 ms) are indicated by vertical dotted lines in each plot.

 ==> different in virtual sensor power could imply attention directed to the stimulus (or the subjects were more vigilant in the correct trials), and thus more likely to perceive the change in speed -- a reasonable explanation? The following is an old fig that aligned to the onset of stimulus in left VF display, the high alpha (around 8 - 12 Hz) shows power difference when stimulus is on. I modified the scripts to get the data in mat format for and will soon modify the figs as soon as the data are generated.



Pfurtscheller, G., C. Neuper, et al. (1994). "Event-related desynchronization (ERD) during visual processing." International Journal of Psychophysiology 16(2-3): 147-153.

Yamagishi, N., N. Goda, et al. (2005). "Attentional shifts towards an expected visual target alter the level of alpha-band oscillatory activity in the human calcarine cortex." Cognitive Brain Research 25(3): 799-809.

Wednesday, December 15, 2010

Right ACC following B (speed change)- Change P = .01

R ACC (13 12  45)  mag. = 0.71   @230 ms






Look up



What is the lower resolutaion in time of the low freq domain... (previous figure)

------------------------

What is happening at the medial activation 60 ms - what is at medial/cingulate activation?
V. van Veen & Carter 2002: following impulsive errors (response made why stimulus evaluation is imcomplete), a large negative deflection (ERN, the detection that an error was made)
==> We did not exclude the correct trials that might be impulsive responses (small response latency)
Caudal ACC:
* frontalcentral N2 prior to the response on correct trials with stimulus conflict, 340 - 380 ms after onset. (response latency 450 - 500 ms)
* ERN immediately following error response (40 - 80 ms)

Rostral area of ACC:
* error related positivity peaking at 200 -250 ms following ERN


ACC is also strongly activated during "guilty knowledge" & "lies" 


Actually the medial frontal/ACC activation magnitude at 50 ms is higher (reported as superior frontal gyrus, more medial 2 voxel superior to the peak found at 60 ms, spatial resolution 2.5 mm):
@50 ms (-10 11 55) mag = 0.73
@60 ms (-18 10 50) mag = 0.68 








HBM - do  methods section...


Write abstract - than make figures that prove the story.