[Mne_analysis] Mne_analysis Digest, Vol 97, Issue 4

[Anja Thiede]

Hi Peng,

 

I have encountered similar problems with this command before, so in case you dig into the source code and find a good solution, please share it with the MNE community!

 

Thanks and best regards,

Anja Thiede

 

 

_________________________________________________________________________

Anja Thiede, M.Sc.

Doctoral student

Cognitive Brain Research Unit (CBRU)

Department of Behavioural Sciences

University of Helsinki

E-Mail: anja.thiede at helsinki.fi

 

 

 

 

From: mne_analysis-bounces at nmr.mgh.harvard.edu [mailto:mne_analysis-bounces at nmr.mgh.harvard.edu] On Behalf Of Hari Bharadwaj
Sent: 13. helmikuuta 2016 19:46
To: Discussion and support forum for the users of MNE Software <mne_analysis at nmr.mgh.harvard.edu>
Subject: Re: [Mne_analysis] Mne_analysis Digest, Vol 97, Issue 4

 

Hi Peng,

 

mri_watershed is part of freesurfer: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed

 

The (large) freesurfer code repository can be downloaded if you wish to do so: https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS

 

 

mne.bem is this module:

https://github.com/mne-tools/mne-python/blob/master/mne/bem.py

 

HTH,

Hari

 

 

Hari Bharadwaj

Research Fellow,

Martinos Center for Biomedical Imaging,

Massachusetts General Hospital

Charlestown, MA 02129

 

hari at nmr.mgh.harvard.edu <mailto:hari at nmr.mgh.harvard.edu> 

www.haribharadwaj.com <http://www.haribharadwaj.com> 

Ph: 734-883-5954


On Feb 13, 2016, at 12:19 PM, Peng Zan <zanpeng.pz at gmail.com <mailto:zanpeng.pz at gmail.com> > wrote:

Sorry, I meant in the 'bin/' directory of mne package, mne_watershed_bem called the function of mri_wathershed, while in mne_watershed.py, function 'mne.bem' is called. Where can I find those two files if I want to check the algorithm in detail. 

 

Thank you very much!

 

Best,

Peng

 

On Sat, Feb 13, 2016 at 12:09 PM, Peng Zan <zanpeng.pz at gmail.com <mailto:zanpeng.pz at gmail.com> > wrote:

Thanks, Alex! 

 

I saw it but it has a major cited function of mri_watershed, which is the key to mne_watershed. My point is where I can find the source code of mri_watershed?

 

Thank you very much!

 

Best,

Peng

 

On Sat, Feb 13, 2016 at 12:00 PM, <mne_analysis-request at nmr.mgh.harvard.edu <mailto:mne_analysis-request at nmr.mgh.harvard.edu> > wrote:

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Today's Topics:

   1. Re: mne_watershed_bem problems (Alexandre Gramfort)


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Message: 1
Date: Fri, 12 Feb 2016 21:45:21 +0100
From: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr <mailto:alexandre.gramfort at telecom-paristech.fr> >
Subject: Re: [Mne_analysis] mne_watershed_bem problems
To: Discussion and support forum for the users of MNE Software
        <mne_analysis at nmr.mgh.harvard.edu <mailto:mne_analysis at nmr.mgh.harvard.edu> >
Message-ID:
        <CADeotZrVB6BCJuxfD2NT5VAXUgSzSw1+Gg8na9L+pzJMOB_Y_g at mail.gmail.com <mailto:CADeotZrVB6BCJuxfD2NT5VAXUgSzSw1%2BGg8na9L%2BpzJMOB_Y_g at mail.gmail.com> >
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hi,

see :

https://github.com/mne-tools/mne-python/blob/master/mne/commands/mne_watershed_bem.py

it's the code we use that is based on freesurfer commands.

HTH
Alex


On Fri, Feb 12, 2016 at 12:41 AM, Peng Zan <zanpeng.pz at gmail.com <mailto:zanpeng.pz at gmail.com> > wrote:
> Dear MNE experts,
>
> I am currently doing mne analysis and came into the problem with
> mne_watershed_bem. From this command, three files of inner and outer skull
> and outer skin surface were generated, but the outer skull reached outside
> of the outer skin surface so I was not able to go on to construct the the
> bem model and then the forward solution. Do you know what is the reason
> causing this error? And how do I fix this? Besides, I could not find the
> source code for mri_watershed command, which has its binary codes in the MNE
> package. Where can I find the source file, and how could I edit the
> algorithm to make any changes to MNE toolbox?
>
> Thank you very much!
>
> Best,
> Peng
>
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