Hi Baris,
On Mar 11, 2016, at 11:13 PM, Demiral, Sukru (NIH/NIAAA) [F] wrote:
> Hi there,
>
> I was wondering what type of instruction was given to MEG subjects for the
> eyes open resting state recordings. Was it documented?
Yes you can find all the details in the HCP reference manual
(HCP_S900_Release_Reference_Manual.pdf page 50). As you can find there "during
the scan the subject is supine, padded for comfort, instructed to relax with
eyes open and maintain fixation on a projected red crosshair on a dark
background (presented in a darkened room)"
You can find a very detailed explanation of all the acquisition steps and
instructions in the Appendix IV HCP_S500+MEG2_Release_Appendix_IV.pdf.
> Did anyone in the MEG group do a quality assurance of whether subjects really
> kept their eyes open, and reported that?
Yes, we had a set of quality checks in order to address this issue. First of
all the acquisition team was monitoring the subject behavior during
acquisition. Moreover, at the end of the icaclass pipeline a visual inspection
of the ICA results and of the ECG and EOG signals has been done for several
purposes. During this step, the EOG signals were monitored as well as IC
corresponding to eyes movements.
> I looked at some subjects, and realized that they did not blink much; some
> ways they might have kept their eyes closed, making the resting state ‘eyes
> closed’ not eyes open.
I have done the QC of all the subjects and I can say that there are subjects
with poor eyes movements and it is normal. According to my experience, some
subject, probably misunderstanding the instruction, can try to stay with eyes
open during all the acquisition and do not blink if not really necessary. If
you have some particular case please let me know the subject number.
> In addition, when I opened the raw file (c, rfDC) with SPM, it shows the EOG
> channel labels differently than when I open the file with sat Brainstorm. I
> wonder what the best way is to visualize and export the EOG vertical and
> horizontal channels (and also ECG) time series in fileldtrip. Or to put it
> another way, how can I get the finalized physiological channels’ time series
> (with their correct labels) ? I found the script “hcp_exgmontage.m”, shall I
> use this one?
You can use part of the icaclass pipeline if you would like to use
matlab/fieldtrip.
Around line 150 you can find instructions like
montage = hcp_exgmontage(subjectid, experimentid, scanid);
dataELEC=ft_selectdata(dataraw,'channel',montage.labelorg);
dataELECnew=ft_apply_montage(dataELEC,montage);
If you would like to process the ref data has done in the HCP release (i.e
filtering, bad channels and bad segments) you can use all the code you have in
icaclass pipeline until line 232 by avoiding the part of the ICA decomposition
which is time demanding.
The resulting ref channels are in the variable ref_data (line 232). Of course
you can change the parameter has you want.
> Also, Is there an ICA component written out which is classified as blink or
> ECG component?
Yes. The result of the icaclass pipeline contains all the components and the
classification of them in brain, generic artifacts and eog/ecg related ones.
For each session you can find the eog and ecg related artifacts in the
icaclass_vs output files (177746_MEG_3-Restin_icaclass_vs.txt as an example).
You can find the same info in the icaclass_vs.mat file in the class variable.
This is the content of the ASCII files
vs.good = [17 32];
vs.bad = [];
vs.total_ic_number = 37;
vs.brain_ic_number = 30;
vs.brain_ic = [2 3 4 5 6 7 8 9 10 11 12 13 14 15 18 19 20 21 22 23 25 27 28 30
31 33 34 35 36 37];
vs.ecg_eog_ic = [1 16 26 29];
vs.flag = 1;
vs.physio = [];
vs.brain_ic_vs_number = 32;
vs.brain_ic_vs = [2 3 4 5 6 7 8 9 10 11 12 13 14 15 17 18 19 20 21 22 23 25 27
28 30 31 32 33 34 35 36 37];
The variable you are interested in is vs.ecg_eog_ic which contains the indices
of the independent components related to ecg and eog artifacts.
Let me know if you have any further comments or questions,
Best,
Francesco
>
> Thanks very much in advance,
>
> Baris
>
>
> Sukru Baris Demiral, Ph.D.
> Laboratory of Neuroimaging (LNI)
> National Institute on Alcohol Abuse and Alcoholism (NIAAA)
> National Institutes of Health
> 10 Center Drive, Room B2L124
> Bethesda, MD 20892-1013
> Office: 301-402-5861
> Cell: 314-681-0655
>
> _______________________________________________
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>
Francesco Di Pompeo, PhD
Institute of Advanced Biomedical Technologies and
Department of Neuroscience and Imaging
University of Chieti "G. d'Annunzio"
Via dei Vestini - Campus Universitario
66013 Chieti - ITALY
ph: +39-0871-3556907
fax:+39-0871-3556930
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