[Mne_analysis] Mne_analysis Digest, Vol 97, Issue 4

[Alexandre Gramfort]

hi,

the --atlas option does not help?

Alex

On Mon, Feb 15, 2016 at 9:32 AM, Anja Thiede <anja.thiede at helsinki.fi> wrote:
> 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
>
> www.haribharadwaj.com
>
> Ph: 734-883-5954
>
>
> On Feb 13, 2016, at 12:19 PM, Peng Zan <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> 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>
> wrote:
>
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> Today's Topics:
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>    1. Re: mne_watershed_bem problems (Alexandre Gramfort)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 12 Feb 2016 21:45:21 +0100
> From: Alexandre Gramfort <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>
> Message-ID:
>         <CADeotZrVB6BCJuxfD2NT5VAXUgSzSw1+Gg8na9L+pzJMOB_Y_g at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> 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> 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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