# MEG-MRI coordinate system alignment

**URL:** <https://mne.discourse.group/t/meg-mri-coordinate-system-alignment/588>\
**Category:** Mailing List Archive (read-only)\
**Tags:** list-archive\
**Created:** [June 2, 2013, 11:31pm UTC](https://mne.discourse.group/t/meg-mri-coordinate-system-alignment/588 "2013-06-02T23:31:49Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [June 2, 2013, 11:31pm UTC](https://mne.discourse.group/t/meg-mri-coordinate-system-alignment/588/1 "2013-06-02T23:31:49Z")

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Hi,

According to the  
manual\<[http://martinos.org/mne/manual/analyze.html#coordinate-frame-alignment](http://martinos.org/mne/manual/analyze.html#coordinate-frame-alignment)\>,  
the MRI-MEG coordinate frame alignment tools included in mne\_analyze  
utilize the 3D digitizer (Polhemus) data acquired in the beginning of each  
MEG/EEG session and the scalp surface triangulation. Specifically what  
scalp surface triangulation is used here? Is this something generated  
during FreeSurfer's recon-all stream, or is it the BEM mesh created with  
mne\_watershed\_bem?

Ultimately, I am trying to understand how to solve this question: I  
recently overwrote my output from mne\_setup\_source\_space,  
mne\_watershed\_bem, and mne\_setup\_forward\_model. Do I need to re-register my  
MEG/MRI data before proceeding to compute the forward solution?

Best wishes,

Vincent Rupp Jr  
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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [June 3, 2013, 11:37am UTC](https://mne.discourse.group/t/meg-mri-coordinate-system-alignment/588/2 "2013-06-03T11:37:38Z")

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Hi,  
&nbsp;&nbsp;&nbsp;It uses whatever "subject-head.fif" surface lives in the Freesurfer  
$SUBJECTS\_DIR/$SUBJECT/bem/ directory. This is usually prepared by  
mne\_watershed\_bem unless you created this using mne\_surf2bem from  
something else.

Also, the answer to your latter question depends on why you replaced the  
surfaces from mne\_watershed\_bem...Assuming your previous registrations  
were with a reasonable head surface, since the number of parameters for  
the MEG head to MRI head transformation is small compared to the number of  
digitizer points, I'd say it is not necessary to re-register.

HTH,  
Regards,  
Hari

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [June 3, 2013, 1:13pm UTC](https://mne.discourse.group/t/meg-mri-coordinate-system-alignment/588/3 "2013-06-03T13:13:15Z")

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hi Vincent,

if you look in:

[https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run\_anatomy\_tutorial.sh](https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run_anatomy_tutorial.sh)

you'll read:

# Make high resolution head surface  
mkheadsurf -s ${SUBJECT}  
mne\_surf2bem --surf ${SUBJECTS\_DIR}/${SUBJECT}/surf/lh.seghead --id 4  
--check --fif ${SUBJECTS\_DIR}/${SUBJECT}/bem/${SUBJECT}-head.fif  
# if the previous command fails you can use the --force option.

if this step succeeds you'll have a high resolution scalp for  
coregistration rather than the BEM surface.

HTH  
Alex

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [June 4, 2013, 5:45pm UTC](https://mne.discourse.group/t/meg-mri-coordinate-system-alignment/588/4 "2013-06-04T17:45:16Z")

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Thanks very much for the help. Great info.

Best wishes,

Vincent Rupp Jr