# questions **URL:** \ **Category:** Mailing List Archive (read-only)\ **Tags:** list-archive\ **Created:** [June 11, 2012, 9:13pm UTC](https://mne.discourse.group/t/questions/454 "2012-06-11T21:13:53Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [June 11, 2012, 9:13pm UTC](https://mne.discourse.group/t/questions/454/1 "2012-06-11T21:13:53Z")
Hi Jeff, We are getting closer. Please make sure to send your emails to the list so that everyone can learn (and help) Dan G. Wakeman wrote: > Hi Matti, > > I followed your instructions as follows: > > Changed time scales to 4-253 ms to avoid flat segments at begin and end > of EEG > Had already done 1-100 Hz bandpass filtering > Marked VREF as bad > Recalculated everything except electrode alignment Does this mean you recalculated the noise covariance matrix and inverse solution? > Loaded average and surfaces back into mne\_analyze > > When viewing inverse results on the inflated surface, they do not look > any different than before, that is: > a. Source activations do not generally match scalp EEG > b. For dSPM and sLORETA, most source activity is confined to R hemi > > Questions: > 1. It looks like I can examine the noise-cov matrix with Matlab ? what > should I see, good or bad? There are some examples (particularly on the webpage www.martinos.org/mne ) > 2. Alex G suggested I use ico5, not ico3. Other than higher spatial > resolution, that should not be cuasing the problems I see (?) Well, it is theoretically possible. ico 3 is very bad for any orientation constraints (which i believe you indicated you were using in an earlier e-mail). It is ok, to user for loose/no orientation constraint, although very misleading. I would never recommend using anything less than ico 5, and even with ico 5 I recommend using the loose variable orientation constraints. > 3. Alex also suggested I use a diagonal noise-cov matrix ? how would I > go about that? If I knew what to put in it, I suppose I could create and > save using Matlab toolbox there is the --diagnoise option in mne\_do\_inverse\_operator > 4. Is there any way to confirm that channel 257 has indeed been > eliminated in the averaging and covariance calculation? Well, did you check the output when re-running the commands. Did it talk about the bad channels detected? It is also possible to check with the MATLAB toolbox. > 5. To that end, I have not been able to view the average EEG ? the > window is blank. Someone suggested I create a new layout, but why can't > the software see the layouts I already created for the raw EEG? It should be able to see them, if you put them in the right directory as described in the manual. You should be able to select it using Adjust -\> Select trace layout... Are you using a noise covariance matrix? What exact command did you use to generate it? How does the time period you used to generate your noise covariance relate to the time period you are trying to invert? Did you make sure that --projon was used when generating your noise covariance matrix? ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [June 11, 2012, 10:18pm UTC](https://mne.discourse.group/t/questions/454/2 "2012-06-11T22:18:50Z")
Dan, see below, thanks, -Jeff > Hi Jeff, > > We are getting closer. Please make sure to send your emails to the list > so that everyone can learn (and help) > > Dan G. Wakeman wrote: > > > Hi Matti, > > > > I followed your instructions as follows: > > > > Changed time scales to 4-253 ms to avoid flat segments at begin and end > > of EEG > > Had already done 1-100 Hz bandpass filtering > > Marked VREF as bad > > Recalculated everything except electrode alignment > > Does this mean you recalculated the noise covariance matrix and inverse > solution? Yes > > Loaded average and surfaces back into mne\_analyze > > > > When viewing inverse results on the inflated surface, they do not look > > any different than before, that is: > > a. Source activations do not generally match scalp EEG > > b. For dSPM and sLORETA, most source activity is confined to R hemi > > > > Questions: > > 1. It looks like I can examine the noise-cov matrix with Matlab ? what > > should I see, good or bad? > > There are some examples (particularly on the webpage www.martinos.org/mne > ) I will look at these, but as I dug into the Matlab script mne\_read\_cov, I found unknown items such as "node" and "kind", and looking deeper at the fif routines I did not yet find enough info to be able to set these. > > 2. Alex G suggested I use ico5, not ico3. Other than higher spatial > > resolution, that should not be cuasing the problems I see (?) > > Well, it is theoretically possible. ico 3 is very bad for any > orientation constraints (which i believe you indicated you were using in > an earlier e-mail). It is ok, to user for loose/no orientation > constraint, although very misleading. I would never recommend using > anything less than ico 5, and even with ico 5 I recommend using the > loose variable orientation constraints. I agree I should not have used fixed orientation with ico3, did not think that through. I will try ico5 and loose orientation > > 3. Alex also suggested I use a diagonal noise-cov matrix ? how would I > > go about that? If I knew what to put in it, I suppose I could create > > and > > save using Matlab toolbox > > there is the --diagnoise option in mne\_do\_inverse\_operator Thanks, I will try that as well > > 4. Is there any way to confirm that channel 257 has indeed been > > eliminated in the averaging and covariance calculation? > > Well, did you check the output when re-running the commands. Did it talk > about the bad channels detected? It is also possible to check with the > MATLAB toolbox. I did not always check, will look in more detail next time > > 5. To that end, I have not been able to view the average EEG ? the > > window is blank. Someone suggested I create a new layout, but why can't > > the software see the layouts I already created for the raw EEG? > > It should be able to see them, if you put them in the right directory as > described in the manual. You should be able to select it using Adjust -\> > Select trace layout... If I can get to them when viewing raw data, I would think they are in the right directory... But I will re-check > Are you using a noise covariance matrix? yes > What exact command did you use to generate it? I did it in mne\_browse\_raw > How does the time period you used to generate your noise covariance > relate to the time period you are trying to invert? Same time periods - full 255 seconds > Did you make sure that --projon was used when generating your noise > covariance matrix? Matti said it was irrelevant as the only projection I would be using is the average ref for EEG > > 6. I do not understand how to set the eegflat value - what should by > > entered? Any suggestion here? -Jeff