[Mne_analysis] forward model having only segmentation files

[Alexandre Gramfort]

Hi Anton,

I agree with Dan. You should work with a volume source space.

It's not going to be trivial but the way to go is:

- extract the BEM surfaces and write them a folder matching
${SUBJECTS_DIR}/${SUBJECT}/bem

see the mne-sample-data for an example of database layout

you'll probably need to have surface in the
${SUBJECTS_DIR}/${SUBJECT}/mri folder to mne_analyze to be able to do
the coregistration.

- then you can run the forward computation see:

https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run_meg_volume_tutorial.sh

- then with python you can run an inverse computation. See:

http://www.martinos.org/mne/auto_examples/inverse/plot_compute_mne_inverse_volume.html

you should then be able to write a nifty or .mgh file to overlay the
activations on the volume e.g. with freeview shipped with freesurfer

may the force be with you !

Alex

On Fri, Mar 9, 2012 at 5:59 PM, dgw <dgwakeman at gmail.com> wrote:
> Hi Anton,
>
> The only thing I can think of would be to use mne_volume_source_space. You
> would still need to generate a couple of surfaces for your BEM, but this
> should not be very difficult. If you need more advice about that, please let
> me know.
>
> D
>
>
> tokariev at mappi.helsinki.fi wrote:
>>
>> Hello Alex,
>>
>> Thank you very much for your reply. I completely understand that it is
>>  better to use Freesurfer first. But I deal with neonatal data. And
>>  Freesurfer, unfortunately, fails to analyse such kind of data (when I
>>  tried it even did not create all folders and files, those i could edit
>>  manually). As far as I got from literature, people (almost) always do
>>  segmentation of neonatal data manually and then launch Freesurfer. But  it
>> takes a lot of time to do and is not trivial task. But I have  already
>> segmentation files done in FSL. So, my idea was somehow to use  them in MNE
>> to get forward model. What would you recommend? What do  you think the most
>> optimal way to act in my case?
>>
>> Regards,
>> Anton
>>
>> Цитирую "Alexandre Gramfort" <gramfort at nmr.mgh.harvard.edu>:
>>
>>> Hello Anton,
>>>
>>> it's doable but it's far from trivial as it requires you to understand
>>> the
>>> internal of the MNE anatomical pipeline (where MNE expects to find
>>> the files etc.). I would seriously consider running freesurfer on my
>>> subject
>>> and rely the automatic / standard pipeline. Freesurfer also gives you
>>> all the segmentations including the cortical surface for sources'
>>> locations.
>>>
>>> Alex
>>>
>>> On Thu, Mar 8, 2012 at 2:31 PM,  <tokariev at mappi.helsinki.fi> wrote:
>>>>
>>>> Dear all,
>>>>
>>>> I want to create forward model in MNE software. But I have only
>>>> segmentation data (skull.mgz, skin. mgz, brain.ngz) got in FSL
>>>> software + EEG electrodes coordinates. Is it possible to do at all? If
>>>> yes, could anyone give me an advice how to do it or refer to some
>>>> tutorial where I could read about. I've read how to do it having 'raw'
>>>> data and using Freesurfer software + MNE. But in my case all I have
>>>> only are segmentation files and file with electrodes positions.
>>>>
>>>> Regards,
>>>> Anton
>>>>
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