Hi Kanad,
I looked through this thread and I suspect you have a noise source that is coming from something other than the eyes. I would be happy to have a look at one of these recordings. If that works for you, please upload the file to somewhere (for example, Dropbox), then send me a link by email where I can download it. You can get my email by clicking on my username on this forum.
Just a few comments/questions:
- How does the MEG/MRI coregistration look? Can you attach a screen shot with the scalp surface and the MEG sensors.
- Are there any noisy channels that you have or have not marked bad?
- What are you using for the noise covariance? Emptyroom or recordings?
- What do you mean by ‘the data looks very clean in both CTF software and with FieldTrip’?
As for the incorrect number of markers in the AUX file, this is normal. Because the AUX file is divided into ‘trials’ not associated with the actual task markers, there can sometimes be extra markers detected, as in the case where a marker spans two ‘trials’ (the end of one and the beginning of an other). The best practice for detecting the correct number of markers in the AUX file is to (1) convert the file to continuous, then (2) re-detect the markers on the stim channel. This will then give you only the onset of each marker.
Thanks,
Beth