# What happens in mne.viz.Brain when plotting fsaverage?

**URL:** <https://mne.discourse.group/t/what-happens-in-mne-viz-brain-when-plotting-fsaverage/10999>\
**Category:** Support & Discussions\
**Tags:** visualization\
**Created:** [March 22, 2025, 9:47pm UTC](https://mne.discourse.group/t/what-happens-in-mne-viz-brain-when-plotting-fsaverage/10999 "2025-03-22T21:47:19Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Long](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/long/32/374_2.png) [@Long](https://mne.discourse.group/u/Long)\
**Post date:** [March 22, 2025, 9:47pm UTC](https://mne.discourse.group/t/what-happens-in-mne-viz-brain-when-plotting-fsaverage/10999/1 "2025-03-22T21:47:19Z")

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Hi,

I have a question about this function mne.vis.Brain() working with fsaverage.  
fsaverage is in the MRI space, so under which coordinate does mne.vis.brain() do the plotting? I think should be the ‘head’ space. If so, then I assume Brain(), in code below, will automatically convert the fsaverage (MRI space) into the ‘head’ space.

brain = mne.viz.Brain(  
“fsaverage”,  
subjects\_dir=subjects\_dir,  
cortex=“low\_contrast”,  
alpha=0.25,  
background=“white”,  
)

Correct me if I am wrong.

Thanks.

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**Author:** ![dasdiptyajit](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/dasdiptyajit/32/4796_2.png) [@dasdiptyajit](https://mne.discourse.group/u/dasdiptyajit)\
**Post date:** [March 22, 2025, 11:28pm UTC](https://mne.discourse.group/t/what-happens-in-mne-viz-brain-when-plotting-fsaverage/10999/2 "2025-03-22T23:28:27Z")

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Hi long,

Have a look at this:

> **[Source alignment and coordinate frames — MNE 1.9.0 documentation](https://mne.tools/stable/auto_tutorials/forward/20_source_alignment.html)**

To your question:  
When you call `mne.viz.Brain(...)`, it **loads the surface geometry** from FreeSurfer and plots it in its **native coordinate frame** : **surface RAS / MRI space**

best,  
Dip

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<div class="post-metadata">

**Author:** ![Long](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/long/32/374_2.png) [@Long](https://mne.discourse.group/u/Long)\
**Post date:** [March 23, 2025, 1:30am UTC](https://mne.discourse.group/t/what-happens-in-mne-viz-brain-when-plotting-fsaverage/10999/3 "2025-03-23T01:30:55Z")

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Thank you Dip for answering my question. But I have a followup question. In 5th code block of this working-with-seeg tutorial: [Working with sEEG data — MNE 1.9.0 documentation](https://mne.tools/stable/auto_tutorials/clinical/20_seeg.html), the plot has two part, first is the plotting of fsaverage, in MRI space as you said:

[brain](https://mne.tools/stable/generated/mne.viz.Brain.html#mne.viz.Brain) = [mne.viz.Brain](https://mne.tools/stable/generated/mne.viz.Brain.html#mne.viz.Brain)( “fsaverage”, [subjects\_dir](https://docs.python.org/3/library/pathlib.html#pathlib.PosixPath)=[subjects\_dir](https://docs.python.org/3/library/pathlib.html#pathlib.PosixPath), cortex=“low\_contrast”, alpha=0.25, background=“white”, )

The next part is the SEEG contacts:  
[brain.add\_sensors](https://mne.tools/stable/generated/mne.viz.Brain.html#mne.viz.Brain.add_sensors)([epochs.info](https://mne.tools/stable/generated/mne.Info.html#mne.Info), trans=trans)  
In above plotting of SEEG electrodes, the trans is calculated as below, which is a transformation to the ‘head’ space:  
trans = mne.channels.compute\_native\_head\_t(montage)  
So, the contacts are actually plotted in the ‘head’ space.

I don’t understand why these two parts are plotted in different space?