[Mne_analysis] forward model having only segmentation files

dgw dgwakeman at gmail.com
Tue Mar 13 10:31:47 EDT 2012
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The easiest thing to do would be to play around with the FreeSurfer 
command mri_watershed

use -surf

For each volume you give it the created outer skin surface will be the 
outermost surface you can use for your bem. Use it serially, re-naming 
the files for use in your BEM. If this is. You may have to play a while 
to get it to work. I suspect you will need to apply the mask to your 
original volume, as it expects non-binary data.

D

tokariev at mappi.helsinki.fi wrote:
> Hi
> 
> I have one more question... Is there any function in MNE/Freesurfer that 
> allows to create automatically inner and outer skull surfaces from 
> binary skull mask (from FSL)? And the same for the binary skin mask? I 
> have difficulties with finding the answer for this question in Internet...
> 
> Regards,
> Anton
> 
> Lainaus "Alexandre Gramfort" <gramfort at nmr.mgh.harvard.edu>:
> 
>> hi anton,
>>
>> for BEM you need inner-skull, outer-skull and outer-skin surfaces
>>
>> you need the gray / white interface for a cortically constrained
>> source space but no need with a volumic source space.
>>
>> Alex
>>
>> On Mon, Mar 12, 2012 at 10:25 AM,  <tokariev at mappi.helsinki.fi> wrote:
>>> Hi Dan and Alex,
>>>
>>> Thank you very much for your advices! I'll try to implement them.
>>>
>>> One more question... do I understand correctly that to be able to create
>>> forward model I will need both boundaries in brain segmentation file: 
>>> outer
>>> cortex/CSF boundary and gray/white junction boundary? If I have only
>>> cortex/CSF boundary I can generate only braine surface but not forward
>>> model?
>>>
>>> Thanks in advance!
>>>
>>> BW,
>>> Anton
>>>
>>>
>>> Lainaus "Alexandre Gramfort" <gramfort at nmr.mgh.harvard.edu>:
>>>
>>>
>>>> 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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