# weighted MNE units

**URL:** <https://mne.discourse.group/t/weighted-mne-units/1973>\
**Category:** Mailing List Archive (read-only)\
**Tags:** list-archive\
**Created:** [October 8, 2019, 8:14am UTC](https://mne.discourse.group/t/weighted-mne-units/1973 "2019-10-08T08:14:20Z")\
**Posts on this page:** 5\
**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:** [October 8, 2019, 8:14am UTC](https://mne.discourse.group/t/weighted-mne-units/1973/1 "2019-10-08T08:14:20Z")

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Hi,

I am using MNE Python to do source modeling with weighted MNE and am wondering about very small units of the sources. This is something that I have found with my own data and could reproduce the issue using the sample data: [https://github.com/athiede13/speech\_sources/blob/master/weighted\_MNE\_sample.py](https://github.com/athiede13/speech_sources/blob/master/weighted_MNE_sample.py)

While I would expect source activations in the range of 30-60 nAm (for example as in dipole solution [https://mne.tools/stable/auto\_examples/inverse/plot\_mixed\_norm\_inverse.html](https://mne.tools/stable/auto_examples/inverse/plot_mixed_norm_inverse.html) that uses the same data), what I get are values in the range of 0.3-0.6 nAm. So there seems to be a difference of 2 orders of magnitude. Do you know where this could come from? I have pondered about this for a while and cannot find the source of the difference.

Thanks for having a look and I hope that we can figure it out!

Best regards,  
Anja Thiede

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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:** [October 8, 2019, 8:50am UTC](https://mne.discourse.group/t/weighted-mne-units/1973/2 "2019-10-08T08:50:38Z")

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Dear Anja,

MNE promotes sources with minimal energy / variance. This leads  
to a bias in the estimated amplitudes. If you care about absolute  
amplitudes you should have a look at dipole fits or sparse solvers  
that estimate multi-dipole configurations.

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:** [October 9, 2019, 5:55am UTC](https://mne.discourse.group/t/weighted-mne-units/1973/3 "2019-10-09T05:55:01Z")

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Thank you Alex for your fast reply! If I understood correctly, then these small values are indeed correct and should be comparable to others obtained with the same method (e.g. for group comparisons), even if they are not the absolute amplitudes. Is that correct? What about the unit, is it indeed Am or should it rather be called an arbitrary unit?

Best regards,  
Anja

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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:** [October 9, 2019, 6:02am UTC](https://mne.discourse.group/t/weighted-mne-units/1973/4 "2019-10-09T06:02:42Z")

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hi,

Thank you Alex for your fast reply! If I understood correctly, then these

> small values are indeed correct and should be comparable to others obtained  
> with the same method (e.g. for group comparisons), even if they are not the  
> absolute amplitudes. Is that correct?

yes

> What about the unit, is it indeed Am or should it rather be called an  
> arbitrary unit?

it is indeed Am when you use MNE.

Alex

> Best regards,
> 
> Anja
> 
> \*From:\* mne\_analysis-bounces at nmr.mgh.harvard.edu [mailto:  
> mne\_analysis-bounces at nmr.mgh.harvard.edu] \*On Behalf Of \*Alexandre  
> Gramfort  
> \*Sent:\* tiistaina 8. lokakuuta 2019 11.51  
> \*To:\* Discussion and support forum for the users of MNE Software \<  
> mne\_analysis at nmr.mgh.harvard.edu\>  
> \*Subject:\* Re: [Mne\_analysis] weighted MNE units
> 
> \* External Email - Use Caution \*
> 
> Dear Anja,
> 
> MNE promotes sources with minimal energy / variance. This leads
> 
> to a bias in the estimated amplitudes. If you care about absolute
> 
> amplitudes you should have a look at dipole fits or sparse solvers
> 
> that estimate multi-dipole configurations.
> 
> HTH
> 
> Alex
> 
> \* External Email - Use Caution \*
> 
> Hi,
> 
> I am using MNE Python to do source modeling with weighted MNE and am  
> wondering about very small units of the sources. This is something that I  
> have found with my own data and could reproduce the issue using the sample  
> data:  
> [https://github.com/athiede13/speech\_sources/blob/master/weighted\_MNE\_sample.py](https://github.com/athiede13/speech_sources/blob/master/weighted_MNE_sample.py)
> 
> While I would expect source activations in the range of 30-60 nAm (for  
> example as in dipole solution  
> [https://mne.tools/stable/auto\_examples/inverse/plot\_mixed\_norm\_inverse.html](https://mne.tools/stable/auto_examples/inverse/plot_mixed_norm_inverse.html)  
> that uses the same data), what I get are values in the range of 0.3-0.6  
> nAm. So there seems to be a difference of 2 orders of magnitude. Do you  
> know where this could come from? I have pondered about this for a while and  
> cannot find the source of the difference.
> 
> Thanks for having a look and I hope that we can figure it out!
> 
> Best regards,
> 
> Anja Thiede
> 
> \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_  
> Anja Thiede, M.Sc.  
> Doctoral student
> 
> Cognitive Brain Research Unit
> 
> Department of Psychology and Logopedics
> 
> Faculty of Medicine
> 
> University of Helsinki
> 
> E-Mail: anja.thiede at helsinki.fi
> 
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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:** [October 9, 2019, 6:11am UTC](https://mne.discourse.group/t/weighted-mne-units/1973/5 "2019-10-09T06:11:10Z")

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Ok, thank you very much for clarifying this!

Best,  
Anja