# Misalignment/coordinate mismatch in source reconstruction

**URL:** <https://mne.discourse.group/t/misalignment-coordinate-mismatch-in-source-reconstruction/11887>\
**Category:** Support & Discussions\
**Created:** [July 13, 2026, 6:27pm UTC](https://mne.discourse.group/t/misalignment-coordinate-mismatch-in-source-reconstruction/11887 "2026-07-13T18:27:23Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![A\_Portier](https://avatars.discourse-cdn.com/v4/letter/a/d2c977/32.png) [@A\_Portier](https://mne.discourse.group/u/A_Portier)\
**Post date:** [July 13, 2026, 6:27pm UTC](https://mne.discourse.group/t/misalignment-coordinate-mismatch-in-source-reconstruction/11887/1 "2026-07-13T18:27:23Z")

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Hello!

I’m a relative beginner with MNE in general and source rec in particular. I’m doing source reconstruction of EEG data using fsaverage as a template (as I don’t have MRI data for my actual subjects).

So, like, pretty basic, I load fsaverage data from MNE, read the source space and solution matrix from those files, and I read my (autorejected, epoched) EEG data with mne.read\_epochs. And then I check the alignment:

```python
fig = mne.viz.plot_alignment(epochs.info, trans="fsaverage", src=src, dig=True, surfaces=dict(brain=0.6, outer_skull=0.4, head=0.1))
mne.viz.set_3d_view(fig, azimuth=0, elevation=90)

```

And I see this:

 ![BCA5CA98-967C-461F-9661-4A5544BD69C3](https://global.discourse-cdn.com/free1/uploads/mne/original/2X/5/58b8ffa07d58d512ec55d3fac87477593cbb30fb.jpeg)

As you can see, while the electrodes are located properly in relation to each other, it looks as though there’s some kind of coordinate mismatch, with the electrodes being located a lot lower than they should be.

Attempting to check I have the right montage with `print(epochs.get_montage().dig)` gives me `[<DigPoint | LPA : (-95.0, 0.0, 0.0) mm : head frame>, <DigPoint | Nasion : (0.0, 95.0, 0.0) mm : head frame>, <DigPoint | RPA : (95.0, 0.0, 0.0) mm : head frame>, <DigPoint | EEG #1 : (-29.4, 90.4, 0.0) mm : head frame>, <DigPoint | EEG #2 : (-51.8, 63.9, 47.5) mm : head frame>, etc.`which doesn’t strike me as strange or unexpected.

I am a bit more puzzled by the transform file itself, as `mne.read_trans("C:/Users/aportier/mne_data/MNE-fsaverage-data/fsaverage/bem/fsaverage-trans.fif")` gives me the following:

```python
<Transform | head->MRI (surface RAS)>
[[0.9999938 -0.00355761 -0.00000057 0.00187336]
 [0.00355187 0.99838907 -0.05662654 -0.02879576]
 [0.00020204 0.05662593 0.99839538 -0.0412941]
 [0. 0. 0. 1.]]

```

But I’m not entirely sure I’m understanding that correctly.

Again, I’m essentially a beginner here, so stupid mistakes wouldn’t be out of character, but what I see is essentially: I used a standard, predefined template that MNE can deal with. While my montage has only 63 channels (one being taken up for a stimulation), it is otherwise a pretty standard montage, and indeed I’ve had no problems with things (like making topomaps, etc.) that required knowing the relative positions of the electrodes.

And yet, something has gone wrong — meaning, probably, that I made a mistake somewhere. Anyone knows where?

Thanks in advance for any help!

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<div class="post-metadata">

**Author:** ![wmvanvliet](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/wmvanvliet/32/100_2.png) [@wmvanvliet](https://mne.discourse.group/u/wmvanvliet)\
**Post date:** [July 14, 2026, 12:53pm UTC](https://mne.discourse.group/t/misalignment-coordinate-mismatch-in-source-reconstruction/11887/2 "2026-07-14T12:53:33Z")

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try setting the montage to `fsaverage_1005`. That should give you electrode positions that are co-registered with the fsaverage template.

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<div class="post-metadata">

**Author:** ![A\_Portier](https://avatars.discourse-cdn.com/v4/letter/a/d2c977/32.png) [@A\_Portier](https://mne.discourse.group/u/A_Portier)\
**Post date:** [July 15, 2026, 6:55am UTC](https://mne.discourse.group/t/misalignment-coordinate-mismatch-in-source-reconstruction/11887/3 "2026-07-15T06:55:45Z")

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Thanks a lot! It worked!

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<div class="post-metadata">

**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [July 22, 2026, 6:55am UTC](https://mne.discourse.group/t/misalignment-coordinate-mismatch-in-source-reconstruction/11887/4 "2026-07-22T06:55:57Z")

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