# Problem including reference electrode in info\['chs'\]\[.\]\['loc'\] **URL:** \ **Category:** Mailing List Archive (read-only)\ **Tags:** list-archive\ **Created:** [December 10, 2015, 10:25pm UTC](https://mne.discourse.group/t/problem-including-reference-electrode-in-info-chs-loc/937 "2015-12-10T22:25:23Z")\ **Posts on this page:** 12\ **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:** [December 10, 2015, 10:25pm UTC](https://mne.discourse.group/t/problem-including-reference-electrode-in-info-chs-loc/937/1 "2015-12-10T22:25:23Z")
Hi Again, I've been debugging my code by comparing an EEG forward model that I constructed using MNE python to one constructed by a former labmate using MNE C. The lead field matrices are different, even when I use identical source space, BEM solution, and transformation file. I've narrowed down the problem to info['chs'][...]['eeg\_loc'], which in the old data is 3x2, with the second column having the location of the reference electrode. In my data, eeg\_loc is 3x1, with no information about the location of the reference electrode. The information in this second column appears to be used by \_bem\_specify\_els, which loops over the columns of the electrode location matrix. I've played around a bit with add\_reference\_channels and set\_eeg\_reference, but neither of them changes the second column in eeg\_loc for the non-reference electrodes. The location of the reference electrode is specified in my montage file (hpts), but there doesn't seem to be a way to apply it to the eeg\_loc of all of the other electrodes. This is what I thought might have worked, but it seems to just add another electrode, without influencing the chs of the other electrodes: montage = mne.channels.read\_montage(montage\_hpts, transform=True, unit='mm') raw = mne.io.read\_raw\_fif(rawfile,preload=True) mne.io.add\_reference\_channels(raw,'EEG000',copy=False) raw.set\_montage(montage) mne.io.set\_eeg\_reference(raw,['EEG000'],copy=False) Thoughts? Thanks, Emily -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20151210/e8f0a9b0/attachment.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20151210/e8f0a9b0/attachment.html) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [December 10, 2015, 10:30pm UTC](https://mne.discourse.group/t/problem-including-reference-electrode-in-info-chs-loc/937/2 "2015-12-10T22:30:50Z")
Hi Emily,     My immediate thought is.. do you have an average reference projector that is being applied in one case and not the other? Hari ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [December 10, 2015, 10:34pm UTC](https://mne.discourse.group/t/problem-including-reference-electrode-in-info-chs-loc/937/3 "2015-12-10T22:34:51Z")
Yes. Well, in the old data the average reference projector's active property is set to 'on', and in my data it is set to 'off'. I tried running mne.io.proj.activate\_proj to make it active in the new data, and it did not affect the lead field matrix. Is there some other way to activate the proj? Emily ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [December 10, 2015, 11:28pm UTC](https://mne.discourse.group/t/problem-including-reference-electrode-in-info-chs-loc/937/4 "2015-12-10T23:28:10Z")
Hi Emily, I think some other developer might be better suited to answer your full question. But are you by any chance looking for raw.apply\_proj()? Best regards, Mainak ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [December 11, 2015, 7:32am UTC](https://mne.discourse.group/t/problem-including-reference-electrode-in-info-chs-loc/937/5 "2015-12-11T07:32:28Z")
Dear Emily, the `set_eeg_reference` and `add_reference_channels` are functions that transform the EEG data. They allow you to specify different referencing schemes, which is useful for sensor level analysis. They also set the `custom_ref_applied` flag in the info structure to explicitly override the average reference projector. Since you are doing source localisation and therefore want the average reference, don?t use these functions, they don?t do what you wanted them to do. Let?s move on to your problem: I was always wondering why `eeg_loc` was a 3x2 matrix? thank you for tracking it down. I think many of our data import routines only set the first row of `eeg_loc`; this should be fixed. However, where in `_bem_specify_els` does it loop over the `eeg_loc` matrix exactly? I can?t find it... regards, Marijn. ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [December 11, 2015, 3:22pm UTC](https://mne.discourse.group/t/problem-including-reference-electrode-in-info-chs-loc/937/6 "2015-12-11T15:22:34Z")
In line 141, \_bem\_specify\_els loops over the columns of el\_r, which is a transformed version of els[...][rmag]. els comes from the coils variable in \_prep\_field\_computation, which come from fwd\_data from \_compute\_forwards, yada yada yada... If you trace it all the way to its source, the field rmag is set through make\_forward\_solution \> \_prep\_channels \> \_create\_coils \> \_create\_eeg\_el, which sets it to a (potentially transformed) version of ch[eeg\_loc]. The reason it matters is that in \_bem\_specify\_els, the sol variable is constructed as a weighted sum of the bem solution at tri vertices near the locations in the columns of rmag. The weight w on the second column (from elw, also set in \_create\_eeg\_el) is -1. So the bem is subtracting off the influence of the reference electrode. Apologies if this is vague -- I'm still familiarizing myself with the theory. At this point I have a better grasp on the code, since I've been stepping through it debugging. Thanks, Emily ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [December 11, 2015, 3:34pm UTC](https://mne.discourse.group/t/problem-including-reference-electrode-in-info-chs-loc/937/7 "2015-12-11T15:34:36Z")
I think the code works properly if the eeg\_loc is set to the correct 3x2 matrix: I reran the forward solution for the old data using MNE python and I get basically the same answer as MNE C (differences on the order of 10^-3, when the lead field matrix entries are on the order of 100). So MNE python is loading the data properly and using it properly. The problem is that I can't create a Raw object using \*only\* MNE python that has the supposedly correct 3x2 eeg\_loc parameters. I think the solution would involve adding the reference electrode to the Montage or the DigMontage, since that's where the information is (at least in my data). In case it matters, I'm getting my Montage from a hpts file that labels the reference as eeg electrode 0. Since that electrode doesn't exist in the recordings, it isn't used by set\_montage. That's why I thought it might work to add the reference electrode using add\_reference\_channels before running set\_montage. Emily ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [December 11, 2015, 3:52pm UTC](https://mne.discourse.group/t/problem-including-reference-electrode-in-info-chs-loc/937/8 "2015-12-11T15:52:46Z")
One more thing: the only place in the documentation that talks about the reference channel location being stored with eeg channel locations is here: [http://martinos.org/mne/stable/manual/c\_reference.html](http://martinos.org/mne/stable/manual/c_reference.html) under the entries for "ch\_pos" in the matlab structures. I'm assuming ch\_pos in the matlab structures serves the same purpose as eeg\_loc in the python info dicts. Emily ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [December 11, 2015, 4:02pm UTC](https://mne.discourse.group/t/problem-including-reference-electrode-in-info-chs-loc/937/9 "2015-12-11T16:02:18Z")
Emily, why do you the location of a reference channel? if you average reference you don't need any extra location. You just need the location of your EEG channels for which you have data. Maybe I miss something Alex ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [December 11, 2015, 4:09pm UTC](https://mne.discourse.group/t/problem-including-reference-electrode-in-info-chs-loc/937/10 "2015-12-11T16:09:45Z")
I'm still hazy on that, actually. What I know is that the answer is different if the data has the reference electrode location vs if it doesn't. Based on where it is used in the code, it seems to be affecting how the BEM model is used in the forward model computation. Also, I'm starting from the assumption that the forward model constructed using MNE C by my former labmate is correct. I'm trying to replicate that result using MNE python. It's possible that the 3x2 representation of the eeg locations from the MNE C constructed files was a mistake either in the code or in my labmate's usage of the software. Emily ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [December 11, 2015, 4:15pm UTC](https://mne.discourse.group/t/problem-including-reference-electrode-in-info-chs-loc/937/11 "2015-12-11T16:15:24Z")
At this point why don't I upload the files that recreate the error. Is there an accepted way to share data files within Martinos? ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [December 11, 2015, 4:25pm UTC](https://mne.discourse.group/t/problem-including-reference-electrode-in-info-chs-loc/937/12 "2015-12-11T16:25:36Z")
Hey Emily, It's probably best to use e.g. DropBox if you can so other devs not at Martinos can also have a look. But please, as usual, make sure your data are appropriately anonymized first before sharing. I'll also email you privately so we can try to iterate on this a bit, and report back to the email list what we figure out. Eric