[Mne_analysis] mne_setup_source_space

[Alexandre Gramfort]

Honestly I have no clue. Certainly matti can answer but if he's busy I can send
you the C-code to have a look.

A

On Wed, Jun 5, 2013 at 5:50 PM, Gustavo Sudre <gsudre at pobox.com> wrote:
> Alex,
>
> Sure thing. I don't have the sphere-inflated versions of these surfaces, so I've been using the spacing option. For example:
>
> mne_setup_source_space --subject mni --surface cortex --overwrite --spacing 3
>
> is the most decimation I can get:
>
> […]
> loaded lh.cortex 2562/40962 selected to source space (approx. spacing = 3 mm)
> […]
>
> Any other spacing bigger than that gives me the same numbers. For example:
>
> […]
> loaded lh.cortex 2562/40962 selected to source space (approx. spacing = 20 mm)
> […]
>
> If I try a different surface, I can get to a smaller (extreme) number of sources, which made me wonder if there was anything specific in the decimation algorithm about the ratio of decimated / original vertices:
>
> mne_setup_source_space --subject mni --surface thalamus --overwrite --spacing 3
> […]
> loaded lh.thalamus 352/3016 selected to source space (approx. spacing = 3 mm)
> […]
>
> but
>
> […]
> loaded lh.thalamus 9/3016 selected to source space (approx. spacing = 20 mm)
> […]
>
> and I can go all the way down to 3 sources… not that I'd do that.
>
> Let me know if you need more details.
>
> Best,
>
> Gus
>
> On Jun 5, 2013, at 11:32 AM, Alexandre Gramfort <gramfort at nmr.mgh.harvard.edu> wrote:
>
>> hi Gus,
>>
>> can you give the lines you typed and be more specific about ico or oct
>> parameters you used.
>>
>> A
>>
>> On Wed, Jun 5, 2013 at 4:12 PM, Gustavo Sudre <gsudre at pobox.com> wrote:
>>> MNE-ers,
>>>
>>> I was wondering if you could clarify what's the cause of the following behavior. I have a triangular mesh surface (.surf) that was created using mne_convert_surfaces from a .tri file. Now, I'd like to only use some of the points on the surface (i.e. decimate it), so I'm using mne_setup_source_space for that. I get a reduction in the number of sources up to spacing = 3 (from 40962 sources to 2562), but anything higher than that gives me the same number of sources. If I plot the "poka-dot" surface, I can see that there is still plenty of room for further decimation.
>>>
>>> Is there anything in the decimation algorithm that prevents further decimation after a certain ratio? Or should I be checking my surface for some specific malformations?
>>>
>>> Note that this is not a MEG problem, so I'm using the terminology of sources mostly to make it easier. The actual issue is simply decimating a surface. I'm just using the MNE tools because I'm familiar with them and this way I don't have to re-code these procedures :) I thought about implementing my own decimation, but if you know of standard algorithms to decimate a surface, preferably already implemented in Python, I'd appreciate it if you could point me to it.
>>>
>>> Best,
>>>
>>> Gus
>>>
>>>
>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>>> contains patient information, please contact the Partners Compliance HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in error
>>> but does not contain patient information, please contact the sender and properly
>>> dispose of the e-mail.
>>>
>