<div dir="ltr"><br>Dear Maria,<br><br>I'm replying on mne_analysis so other people can join in or follow our conversation. Please join if you haven't already (<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/MNE_Analysis">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/MNE_Analysis</a>)<br>
<br><br>On Sun, Aug 3, 2014 at 10:21 AM, Hakonen Maria <<a href="mailto:maria.hakonen@aalto.fi">maria.hakonen@aalto.fi</a>> wrote:<br>><br>> Hi Denis,<br>><br>> I would yet need noise covariance matrixes for roi analysis. I have calculated them with EOG rejections using mne_process_raw as shown below. I wonder if it causes problems if the noise covariance matrixes are claculated with EOG rejections but averaged signals are calculated without EOG rejections (and ica is applied on epochs).<br>
<br><br>I would not see why that would be a problem, it's a good ideat to not estimate the covariance matrix on biological artefacts. Don't you use ICA for handling EOG/ECG? Should be fine then.<br>What I normally do is to compute the noise covariance after applying ICA. That makes things even more matching, e.g., also applying the same amount of rank reduction.<br>
<br>><br>> I can't use rejections because in the sustained field analysis long epochs cause too many rejections. For transient analysis whit shorter epochs EOG rejections worked well. Should I calculate new covariance matrixes for sustained field analysis using data where EOG rejections are not used but ica is applied instead? Any advice would help a lot!<br>
><br><br>Would it make sense to compute your noise cov from preceeding baseline segments?<br>Then you couls simplify things a bit.<br>Apply ICA to your epochs and then use `mne.compute_covariance` on your epochs.<br>FYI in there's also `mne.compute_raw_data_covariance` for raw data.<br>
<br>><br>> This is how I have calculated covariance matrixes: <br>><br>> foreach file ( ah_sentences1b ah_sentences16b ah_sentences1b2 )<br>> mne_process_raw --raw "$file"_raw.fif \<br>
> --digtrig "STI 014" --grad 0 --projon --events "$file"_merged.eve \<br>
> --cov /scratch/braindata/mhhakone/intell/scripts/cov_desc_merged.cov --savecovtag "-merged.cov"<br>> end<br>><br>> where cov_desc_merged.cov:<br>><br>> cov {<br>> name "intell"<br>
><br>> gradReject 3000e-13<br>> magReject 4e-12<br>> eogReject 150e-6<br>> logfile log_averaging<br>><br>> def {<br>> name "all"<br>
> event 1<br>> tmin -0.1<br>> tmax 0<br>> bmin -0.1<br>> bmax 0<br>> }<br>><br>> }<br>><br>
> Thanks,<br>
> Maria<br>><br><div><br></div><div>Hope this helps,</div><div>Denis</div></div>