# mne\_compute\_raw\_inverse gave perfectly correlated source current estimates **URL:** \ **Category:** Mailing List Archive (read-only)\ **Tags:** list-archive\ **Created:** [February 23, 2012, 2:02am UTC](https://mne.discourse.group/t/mne-compute-raw-inverse-gave-perfectly-correlated-source-current-estimates/412 "2012-02-23T02:02:20Z")\ **Posts on this page:** 7\ **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:** [February 23, 2012, 2:02am UTC](https://mne.discourse.group/t/mne-compute-raw-inverse-gave-perfectly-correlated-source-current-estimates/412/1 "2012-02-23T02:02:20Z")
Hello, I am trying to use mne\_compute\_raw\_inverse to project single trial epochs onto the surface. The command finishes without erros, but is generating perfectly correlated source estimates from distant regions. The scale and sign of current estimates differ, but the correlation is either 1 or -1. Below is the command: #do forward solution mne\_do\_forward\_solution --overwrite \ --meas ${s}\_prep\_ave.fif --subject ${s} --fwd ${s}\_prep\_ave\_fwd.fif --meg --eeg      #create inverse operator mne\_do\_inverse\_operator --fwd ${s}\_prep\_ave\_fwd.fif --depth \ --loose 0.2 --meg --eeg --senscov ${s}\_prep\_cov.fif --subject ${s} #project raw data, for each label mne\_compute\_raw\_inverse --in ${s}\_${rn}\_sss\_ds\_raw.fif \ --inv ${s}\_prep\_ave\_fwd.fif-meg-eeg-inv.fif \ --picknormalcomp \ --align\_z \ --labeldir ./ALL-Labels \ --orignames \ --out ${s}-{rn}-label-source However, the same inverse operator worked fine with averaged evoked data, results are reasonable when viewed in mne\_analyze. Any idea what could have gone wrong? Thanks! Kai ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [February 23, 2012, 7:44am UTC](https://mne.discourse.group/t/mne-compute-raw-inverse-gave-perfectly-correlated-source-current-estimates/412/2 "2012-02-23T07:44:27Z")
Hello Kai, a possible explanation is the "nave" used to set the regularization of the inverse problem. if you work with raw data, nave is 1 while with 100 epochs averaged it's 100 and the inverse solution is then far less regularized. A solution is to set the --nave option to a higher value in mne\_compute\_raw\_inverse but you might amplify noise. hope this helps Alex ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [February 23, 2012, 1:02pm UTC](https://mne.discourse.group/t/mne-compute-raw-inverse-gave-perfectly-correlated-source-current-estimates/412/3 "2012-02-23T13:02:04Z")
Hi Alex, I changed --nave to 100 and still got perfect correlations. Actually source estimates look identical between --nave 1 and --nave 100. Any other suggestions? Thanks Kai ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [February 23, 2012, 1:08pm UTC](https://mne.discourse.group/t/mne-compute-raw-inverse-gave-perfectly-correlated-source-current-estimates/412/4 "2012-02-23T13:08:33Z")
hi, did you check that your labels are correct? Alex ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [February 23, 2012, 2:20pm UTC](https://mne.discourse.group/t/mne-compute-raw-inverse-gave-perfectly-correlated-source-current-estimates/412/5 "2012-02-23T14:20:59Z")
Hi Matti and Alex, Yes MEG-only solution worked. Now source estimates are no longer perfectly correlated. Any idea what went wrong regarding including EEG data into the inverse solution? I used labels created by freesurfer's a2009 parcelation, I double checked and they are correct. Thanks! Kai ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [February 23, 2012, 2:40pm UTC](https://mne.discourse.group/t/mne-compute-raw-inverse-gave-perfectly-correlated-source-current-estimates/412/6 "2012-02-23T14:40:35Z")
> Hi Matti and Alex, > Yes MEG-only solution worked. Now source estimates are no longer > perfectly correlated. Any idea what went wrong regarding including EEG > data into the inverse solution? > > I used labels created by freesurfer's a2009 parcelation, I double > checked and they are correct. Are some of the EEG channels dysfunctional and not marked bad? Have you checked the EEG data by switching the average EEG reference off in mne\_browse\_raw? - Matti ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [February 23, 2012, 6:30pm UTC](https://mne.discourse.group/t/mne-compute-raw-inverse-gave-perfectly-correlated-source-current-estimates/412/7 "2012-02-23T18:30:40Z")
Hi Matti, Bad channels were previously marked using mne\_mark\_bad\_channels. I went through the raw data again by turning off EEG reference projection, and added a couple more to the bad list. I also added "eegReject 40e-6" to the covariance file. That worked, now source estimates are no longer perfectly correlated. Thanks! Kai