[Mne_analysis] forward model having only segmentation files

Tue May 29 12:11:42 EDT 2012

Hi Dan,

Thanx for your reply.

Re masks:

Yes, they are binary masks. But I set '1' values to suitable for  
Freesurfer data (to 110). As far as I know Freesurfer does not work  
with binary data. 'Skin mask' is a contour of skin: on the black  
background is a 1 pixel width countour that repeats skin countour  
(each pixel = 110). 'Skull mask' has the same principle but with other  
width.

Re -autorecon1:

I have done like you wrote. I used 'skin' volume for test. I got in  
folder 'mri' next files:
error.log
mri_nu_correct.mni.log
nu.mgz
orig
orig.mgz
rawavg.mgz
T1.mgz
transforms

Folder 'transforms' contains files:
bak
talairach.auto.xfm
talairach_avi.log
talairach_avi_QA.log
talairach.xfm
talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt

BW,
Anton

Lainaus dgw <dgwakeman at gmail.com>:

> Hi Anton,
>
> Well mri_watershed is not designed to deal with segmented data. You  
> need to trick it.
>
> tokariev at mappi.helsinki.fi wrote:
>> 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
> Are these binarized masks? Are they masked at all?
>
> Regardless, you need to put a raw MRI volume saved as 001.mgz in  
> /subjects/subject/mri/orig/001.mgz and run autorecon1 (check  
> freesurfer wiki for details).
>
>>
>> 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?
> First run the above, and let me know what the files are then we can  
> look into the subsequent steps (this is a non-standard hack I  
> developed), so it will take some time to work through.
>
> D
>>
>> 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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