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Dear Flavia,

There are plug-ins in the artefact tool for detecting ECG peaks and eyeblinks and you can specify the input channels for that by type and that's where the ECG and EOG types are useful. Subsequently you can either use that to reject trials or do topography-based artefact correction (see chapter 40 in the manual).

Best,

Vladimir

On Fri, Nov 27, 2015 at 2:55 AM, Flavia Di Pietro <[log in to unmask]> wrote:
Hi Vladimir,

I just wish to clarify something with you regarding artefacts. At this stage I am manually marking/rejecting artefacts - using the Display standard/scalp function or using the Fieldtrip Visual Artefact rejections.

I collect ECG and EOG data in my experiment. 

I am a little unsure as to how ECG and EOG artefacts are taken into account, i.e. how is the ECG and EOG data used by SPM? When I specify my channel types, or make a montage with EOG and ECG incorporated, is this how SPM uses this information?

When I visually inspect my montaged, filtered, downsampled, epoched data I can't see any obvious cardiac patterns, but I certainly see eye blinks in, for example, FP1 and FP2. Is it then a case of manually removing these trials?

I hope I have made sense here! Basically I am wondering about the value of collecting ECG and EOG - how I inform SPM of this information.

Thanks Vladimir,

Flavia


Flavia Di Pietro, PhD
Postdoctoral Research Associate
Neural Imaging Laboratory
Sydney Medical School
University of Sydney
From: Flavia Di Pietro
Sent: 26 October 2015 10:33

To: Vladimir Litvak
Subject: RE: [SPM] SPM for EEG

Dear Vladimir,

Thanks very much indeed for your response. Great, I'll work through that chapter of the manual (I believe you are referring to Chapter 32?) and I hope it will answer my questions.

As always I appreciate your time.

Kind regards,

Flavia

Flavia Di Pietro, PhD
Postdoctoral Research Associate
Neural Imaging Laboratory
Sydney Medical School
University of Sydney
From: Vladimir Litvak [[log in to unmask]]
Sent: 23 October 2015 18:09
To: Flavia Di Pietro
Subject: Re: [SPM] SPM for EEG

Dear Flavia,

Yes, you are completely right. You can go straight to 2nd level analysis. Look at the multimodal faces tutorial chapter for some examples.

Best,

Vladimir

On Fri, Oct 23, 2015 at 6:17 AM, Flavia Di Pietro <[log in to unmask]> wrote:

Dear Vladimir,


I hope you are well. Thanks to your help I can now get power spectra for every channel in both conditions in my subjects. I just have a few questions regarding what do next from that step.


My aim is to compare power between subjects (pain patients and healthy controls). Ideally I would like to look at the power difference between groups in the different frequency bandwidths (i.e. theta, alpha and beta) and I would also like to see if there are any specific sites with differences between the groups.


I am a little confused as to whether I need to run a first-level analysis on my EEG data. It would seem, from the SPM manual and your 2011 reference, that one can proceed to second-level analysis straight after conversion from EEG data to image files. Am I correct in my interpretation of this? Or is first-level analysis still required to evaluate the difference between conditions in one individual subject?


Given that my aim is so simple, I gather I do not need to do any source reconstruction etc. I just put my converted and smoothed images into the first or second-level analysis (as above), then proceed to estimate and results? I'm not sure how many further steps are required for my purposes.


Again, thank you for your help and your patience – being the only one working on EEG in my lab I do rely on the SPM group’s help, and it is always much appreciated.


Flavia



Flavia Di Pietro, PhD
Postdoctoral Research Associate
Neural Imaging Laboratory
Sydney Medical School
University of Sydney
From: Vladimir Litvak [[log in to unmask]]
Sent: 31 July 2015 13:47

To: Flavia Di Pietro
Subject: Re: [SPM] SPM for EEG

Dear Flavia,

This depends on the kind of artefacts you might have. Robust averaging can only remove the artefacts that lead to amplitude outliers but there may also be other kinds. The best way is to experiment and see for yourself.

Best,

Vladimir




On 31 Jul 2015, at 12:53, Flavia Di Pietro <[log in to unmask]> wrote:

Hi Vladimir,

I hope you enjoyed your/are enjoying your Sydney stay.

Thanks, I do have a question for you: do you believe that it is acceptable to leave out the artefact detection stage of pre-processing, and simply perform robust averaging alone?

Thank you!

Flavia



Flavia Di Pietro, PhD
Postdoctoral Research Associate
Neural Imaging Laboratory
Sydney Medical School
University of Sydney
From: Vladimir Litvak [[log in to unmask]]
Sent: 27 July 2015 13:31
To: Flavia Di Pietro
Subject: Re: [SPM] SPM for EEG

I can see it myself as I'm in Sydney at the moment ;-)

Let me know if you have any further questions.

Vladimir 




On 27 Jul 2015, at 08:54, Flavia Di Pietro <[log in to unmask]> wrote:

Dear Vladimir,

As always, thank you for your help. I really appreciate it.

Best regards from Sunny Sydney,

Flavia

Flavia Di Pietro, PhD
Postdoctoral Research Associate
Neural Imaging Laboratory
Sydney Medical School
University of Sydney
From: Vladimir Litvak [[log in to unmask]]
Sent: 26 July 2015 00:51
To: Flavia Di Pietro; [log in to unmask]
Subject: Re: [SPM] SPM for EEG

Dear Flavia,

You can use the 'Spectrum' option in the time-frequency module. Then if you use scalp x frequency option when exporting to images you will get 3D images. If you use just 'frequency' you'll get 1D images averaged over channels. 

Best,

Vladimir

On Sat, Jul 25, 2015 at 1:02 PM, Flavia Di Pietro <[log in to unmask]> wrote:
Dear Vladimir.

Thanks to your help I was able to assign channel locations to my EEG data. Thanks also for the SPM UCL videos online - they are extremely useful for those of us who are so far away!

I am hoping you might be able to provide me with a bit of guidance. Our EEG study is very simple - we are measuring eyes open and eyes closed conditions only. We are measuring this in chronic pain patients and healthy controls. The reason it so simple is that we are associating the EEG measures with MR spectroscopy levels.

So all we really are looking for in the EEG is differences in power. We hypothesise that the patients will display lower frequency activity, and peak activity in lower frequency bands, than in controls. Ideally we will present power in different frequency bands, and also be able to identify any channels/locations that are different between the two groups.

As I understand it, the analysis in SPM can be performed in numerous ways - depending on what it is that you are trying to find and demonstrate in the data.

My question is: how do I (or is it possible to) generate results/graphics of the power across the frequency range in SPM? That is, can I generate global power spectra graphs with frequency along the x-axis and power along the y-axis?

I hope that makes some sense!

Thanks very much indeed, I look forward to hearing from you.

Flavia


Flavia Di Pietro, PhD
Postdoctoral Research Associate
Neural Imaging Laboratory
Sydney Medical School
University of Sydney
From: Flavia Di Pietro
Sent: 18 May 2015 11:16
To: Vladimir Litvak
Subject: RE: [SPM] SPM for EEG

Hello Vladimir,

Thanks very much indeed for your email, and for responding to my query so quickly.

I am going to try your solution today and I will let you know how it goes!

Thanks again.

Kind regards,

Flavia

Flavia Di Pietro, PhD
Postdoctoral Research Associate
Neural Imaging Laboratory
Sydney Medical School
University of Sydney
From: Vladimir Litvak [[log in to unmask]]
Sent: 15 May 2015 18:57
To: Flavia Di Pietro
Cc: [log in to unmask]
Subject: Re: [SPM] SPM for EEG

Dear Flavia,

This indeed indicates that the channel locations were not assigned automatically. There can be several possible reasons for this, the most common are:

1) Your cap (as identified by your channel labels) is not one of those that can be automatically recognised (extended 10-20, biosemi, ant). 
2) You do use extended 10-20 but with too few electrodes (I think you need above 10-15 for it to work). 
3) You have an EGI system where there are different caps for the same channel number so automatic assignment is not possible. 


The solution in all cases is to load the locations file manually (see page 100 in the manual http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf). You can try to find your cap in spm/EEGtemplates directory. That could work for cases 2 and 3 above. If it's not there, you must prepare your own locations file and load it. Then you should follow the steps described in the same chapter to coregister (not necessary if you load from EEGtemplates), project location to 2D, apply and save.

Best,

Vladimir


On Fri, May 15, 2015 at 8:36 AM, Flavia Di Pietro <[log in to unmask]> wrote:

Hi there,


I recently started using SPM for analysis of some EEG data.


I have completed (I think!) all necessary pre-processing steps. Throughout the process, however, I have noticed that in my ‘Display’ function, I am only able to view my channels accurately in the Standard mode, but not in the Scalp mode. Specifically, in the Scalp mode, my channels are not plotted in the 2D space as they are in the manual (on p.360 Version 8 manual) but just in horizontal lines.


This makes me think that I have missed a step (i.e. in informing SPM of my channel locations, for example) or that some error has occurred. I gather if I do not rectify this then I will not be able to do analysis in sensory space etc, later on down the track.


I wonder if anyone else has had this issue, or can shed any light?


Thanks in anticipation!


Flavia


Flavia Di Pietro, PhD
Postdoctoral Research Associate
Neural Imaging Laboratory
Sydney Medical School
University of Sydney