[Mne_analysis] forward model having only segmentation files

tokariev at mappi.helsinki.fi tokariev at mappi.helsinki.fi
Mon May 28 07:15:29 EDT 2012
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Hello,

I am trying to create surfaces for BEM. I have done next steps:

1. I have raw MRI images (DICOM). I did segmentation of inner/outer  
skull and outer skin manually. After this, I changed the original MRI  
images to segmented volumes (to keep all DICOM headers). In other  
words, I got MRI images, where instead of original MRI I put inner  
skull segmentation (also I have saved files like that to outer skull  
and outer skin). Each value of the segmented volume were set to 110.

2. I used mri_convert to get from 3 sets of images in DICOM format,  
those contain segmentations, volumes in .mgz format. So I got  
inner_skull.mgz, outer_skull.mgz and outer_skin.mgz. I put these files  
to the folder: .../freesurfer/subjects/subject/mri/orig

Now I am trying to get surfaces with a help of the command  
'mri_watershed -surf'. I am using it like this: mri_watershed -surf  
inner_skull.mgz inner_skull_surf... But the program fails to create  
surfaces. What I am doing wrong on this stage? Could anyone give an  
advise?

Best wishes,
Anton

Lainaus dgw <dgwakeman at gmail.com>:

> 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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