Thanks to everybody for your input. It is interesting to see that  
different sites see the same type of noise, and the different methods  
people have used to deal with it. I'm still waiting on SSS experts to  
answer some of the questions, though.

Regarding some of the e-mails that were sent: yes, I also see the  
glitches in empty room. I am somewhat against discarding the whole  
channel unless it exhibits the behavior for several repetitions. But  
with 306 other channels, and if this was the only faulty one, it may  
be the case that it's better to discard the channel and keep the  
repetition. Also, it is still unknown how reliable the signal is for  
that channel in the other repetitions.

I'll play with the de-noising methods mentioned, and I'll let you know  
what I find. Let me know if anything else comes to mind.

Thanks,

Gus

On Feb 27, 2009, at 12:01 PM, Max Garagnani wrote:

> Hello,
>
> For the sake of statistical power of this survey -- I did just like  
> Marina (see below).
>
> Max
>
> Marina Papoutsi wrote:
>>
>> Dear Gus,
>>
>> I've also come across this type of artifacts. I am also not sure  
>> about their source. I am skeptical of including those channels in  
>> the data and have treated them as bad channels during maxfilter  
>> processing. I then used SSS -st 4 and that was all.
>>
>> Good luck,
>> Marina
>>
>> Gustavo Sudre wrote:
>>> Jason,
>>>
>>> Thanks for your reply. I did try Maxfilter with -st 4 and -st 10,  
>>> but the jumps were still there. I'm using the default -corr value,  
>>> though. What parameters did you find to get rid of the jumps?
>>>
>>> Best,
>>>
>>> Gus
>>>
>>> On Feb 27, 2009, at 10:21 AM, Jason Taylor wrote:
>>>
>>>> Hi Gustavo,
>>>>
>>>> I've seen those 'jumps' in raw data as well, though I'll leave it  
>>>> to the experts to explain their origin. Have you tried using the  
>>>> MaxFilter -st option? Whereas standard SSS seems to smear sensor  
>>>> jumps over several channels, I've found that SSS-st nicely  
>>>> removes this type of sensor noise.
>>>>
>>>> Cheers,
>>>> - Jason.
>>>>
>>>>
>>>> On Fri, Feb 27, 2009 at 2:59 PM, Gustavo Sudre <[log in to unmask]>  
>>>> wrote:
>>>> Sorry... here's the figure.
>>>>
>>>> Thanks,
>>>>
>>>> Gus
>>>>
>>>>
>>>>
>>>>
>>>> Begin forwarded message:
>>>>
>>>> From: Gustavo Sudre <[log in to unmask]>
>>>> Date: February 27, 2009 9:57:18 AM EST
>>>> To: [log in to unmask]
>>>> Subject: discontinuity in raw data
>>>>
>>>> Hello,
>>>>
>>>> For many repetitions in my experiments I have observed a  
>>>> discontinuity in the raw MEG data. This happens in some of my  
>>>> individual trials, and it is not always across several channels  
>>>> simultaneously. The attached picture shows an example of this  
>>>> type of noise, for a particular trial and channel. When I notice  
>>>> such pattern during recordings, reheating the sensor usually  
>>>> works. However, I don't catch them all the time, so it's often  
>>>> the case that I see this pattern in recorded data. These are my  
>>>> questions:
>>>>
>>>> 1)  What causes this noise? Can the channel be "trusted" even if  
>>>> it shows the pattern a few times?
>>>>
>>>> 2) If I run my data through SSS, this pattern seems to appear in  
>>>> many more channels. That means that I need to discard many more  
>>>> repetitions after running SSS. Is this something intrinsic to the  
>>>> SSS algorithm (i.e. to multiply this noise)? What is the reason  
>>>> for it to appear across more channels after SSS?
>>>>
>>>> 3) If I clean up my raw data prior to SSS (e.g. discard the  
>>>> repetitions with such pattern), and create a new FIF raw file  
>>>> from this new data, my data won't be continuous in time anymore.  
>>>> I don't think SSS will have a problem with it (unless I use the  
>>>> temporal extension). Is that correct?
>>>>
>>>> 4) Would you suggest a more accurate way to deal with these  
>>>> discontinuities (eg. wavelets?), instead of discarding (sometimes  
>>>> precious) trials?
>>>>
>>>> 5) Assuming SSS has no problems with this new "clean" raw file,  
>>>> can the SSS algorithm create such discontinuities by itself? If  
>>>> so, why?
>>>>
>>>> Thanks,
>>>>
>>>> Gus
>>>>
>>>>
>>>>
>>>>
>
> -- 
>
> Max Garagnani, PhD
> MRC - Cognition and Brain Sciences Unit
> 15 Chaucer Rd., Cambridge - CB2 7EF
> U.K.
> http://www.mrc-cbu.cam.ac.uk/people/max.garagnani/
> Tel. +44 1223 355294 (ext. 290)
> Fax: +44 1223 359062