# BIDS pipeline: update anatomical landmarks after coregistration

**URL:** <https://mne.discourse.group/t/bids-pipeline-update-anatomical-landmarks-after-coregistration/11483>\
**Category:** Support & Discussions\
**Created:** [September 11, 2025, 2:26pm UTC](https://mne.discourse.group/t/bids-pipeline-update-anatomical-landmarks-after-coregistration/11483 "2025-09-11T14:26:20Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![sophie](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/sophie/32/3270_2.png) [@sophie](https://mne.discourse.group/u/sophie)\
**Post date:** [September 11, 2025, 2:26pm UTC](https://mne.discourse.group/t/bids-pipeline-update-anatomical-landmarks-after-coregistration/11483/1 "2025-09-11T14:26:20Z")

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Hello!

We formatted freshly recorded MEG & anatomical MRI data to BIDS and then used the mne-bids-pipeline (1.9), as well as manual co-registration using the gui.

Do I remember correctly that we need to update the anatomical landmarks in the BIDS dataset manually using `mne_bids.get_anat_landmarks` and `mne_bids.update_anat_landmarks`?  
Is this documented somewhere? If not, I think we should add it.

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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:** [September 12, 2025, 7:29pm UTC](https://mne.discourse.group/t/bids-pipeline-update-anatomical-landmarks-after-coregistration/11483/2 "2025-09-12T19:29:00Z")

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Hi Sophie,

I don’t have time to look into this now in detail, but I believe you’re right. This was always a bit of a crux ☹ I’d love the re-imagine this entire workflow somehow; for example, what if doing the coregistration would update the BIDS data automatically? 🤔

Richard

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**Author:** ![sophie](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/sophie/32/3270_2.png) [@sophie](https://mne.discourse.group/u/sophie)\
**Post date:** [September 16, 2025, 7:49am UTC](https://mne.discourse.group/t/bids-pipeline-update-anatomical-landmarks-after-coregistration/11483/3 "2025-09-16T07:49:15Z")

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+1 for making the coregistration part of the pipeline (it currently is not). maybe with a config parameter that switches to an interactive mode to be able to use the gui. I will work on the code we use and see whether we can make a suggestion / PR.

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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:** [September 17, 2025, 8:17am UTC](https://mne.discourse.group/t/bids-pipeline-update-anatomical-landmarks-after-coregistration/11483/4 "2025-09-17T08:17:49Z")

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I guess I was more thinking about something along the lines of `mne-bids coregistration`, but then realized that we first need to run FreeSurfer… so yes, maybe doing it via MNE-BIDS-Pipeline does make more sense.

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**Author:** ![sophie](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/sophie/32/3270_2.png) [@sophie](https://mne.discourse.group/u/sophie)\
**Post date:** [September 17, 2025, 8:36am UTC](https://mne.discourse.group/t/bids-pipeline-update-anatomical-landmarks-after-coregistration/11483/5 "2025-09-17T08:36:35Z")

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I thought about adding it to the freesurfer-commands (05), right after creating coregistration surfaces. that makes it kind of more optional.