# Validating correct fiducial coregistration

**URL:** <https://mne.discourse.group/t/validating-correct-fiducial-coregistration/8955>\
**Category:** Support & Discussions\
**Tags:** source-localization, coregistration\
**Created:** [June 18, 2024, 7:05pm UTC](https://mne.discourse.group/t/validating-correct-fiducial-coregistration/8955 "2024-06-18T19:05:33Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![tbonesung](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/tbonesung/32/3365_2.png) [@tbonesung](https://mne.discourse.group/u/tbonesung)\
**Post date:** [June 18, 2024, 7:05pm UTC](https://mne.discourse.group/t/validating-correct-fiducial-coregistration/8955/1 "2024-06-18T19:05:33Z")

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Hello, I am trying to do EEG source localization and I was wondering if the initial step of coregistration needs to be fixed since the fiducials are hovering over the head model like this:

 ![coregistration](https://global.discourse-cdn.com/free1/uploads/mne/original/2X/f/f7c4dd5540ab430700045c3e77ee502e5e34f339.jpeg)

I have a json file of the anatomical landmark coordinates (NAS, LPA, RPA), and a tsv file of 64 digitized EEG sensor locations.

```python
# read electrodes.tsv
custom_montage = mne.channels.read_custom_montage(elec_dir)
info.set_montage(custom_montage)

# read fiducials
fiducial_dict = json.load(open(fname_fiducials))

# Coregistration
coreg = Coregistration(info, subject, subjects_dir, fiducials=fiducial_dict)
fig = mne.viz.plot_alignment(info, trans=coreg.trans, **plot_kwargs)

```

Is there something wrong with my data, or do I need to align the fiducials more?  
Thank you in advance!

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**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\
**Post date:** [June 18, 2024, 8:01pm UTC](https://mne.discourse.group/t/validating-correct-fiducial-coregistration/8955/2 "2024-06-18T20:01:10Z")

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Hello, do you actually have measured electrode locations? Or is this a standard / template montage you’re loading? Do you have individual MRI scans?

Best wishes,  
Richard

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**Author:** ![tbonesung](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/tbonesung/32/3365_2.png) [@tbonesung](https://mne.discourse.group/u/tbonesung)\
**Post date:** [June 18, 2024, 8:07pm UTC](https://mne.discourse.group/t/validating-correct-fiducial-coregistration/8955/3 "2024-06-18T20:07:37Z")

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Hello Richard,

1. Yes, the dataset (open source dataset) has the measured electrode locations (x, y, z) in a tsv file. That is why I read it directly with `mne.channels.read_custom_montage`
2. Yes, each subject has individual T1 images.
3. Fiducials locations were also recorded for each subject, and was directly read from the files

Thank you for your prompt response!

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<div class="post-metadata">

**Author:** ![richard](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/richard/32/15_2.png) [@richard](https://mne.discourse.group/u/richard)\
**Post date:** [June 19, 2024, 7:25am UTC](https://mne.discourse.group/t/validating-correct-fiducial-coregistration/8955/4 "2024-06-19T07:25:21Z")

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Thanks for the clarifications, @tbonesung! Unfortunately I currently don’t have time to provide further assistance; I’m pinging @larsoner and @wmvanvliet, maybe they can give you a hand!

Best of luck,  
Richard

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**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:** [June 19, 2024, 8:16am UTC](https://mne.discourse.group/t/validating-correct-fiducial-coregistration/8955/5 "2024-06-19T08:16:48Z")

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That the nasion point is floating can be attributed to the fact that the MRI has been de-faced. But that LPA and RPA are floating like that seems to indicate a scaling issue. You can use `mne.gui.coregistration` to launch a GUI that allows you to fix the coregistration, including scaling, rotating, etc.