[Mne_analysis] Mne_analysis Digest, Vol 97, Issue 4

[Hari Bharadwaj]

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:
>>> Send Mne_analysis mailing list submissions to
>>>         mne_analysis at nmr.mgh.harvard.edu
>>> 
>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>         https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>> or, via email, send a message with subject or body 'help' to
>>>         mne_analysis-request at nmr.mgh.harvard.edu
>>> 
>>> You can reach the person managing the list at
>>>         mne_analysis-owner at nmr.mgh.harvard.edu
>>> 
>>> When replying, please edit your Subject line so it is more specific
>>> than "Re: Contents of Mne_analysis digest..."
>>> 
>>> 
>>> Today's Topics:
>>> 
>>>    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
>>> >
>>> > _______________________________________________
>>> > Mne_analysis mailing list
>>> > Mne_analysis at nmr.mgh.harvard.edu
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>> >
>>> >
>>> > The information in this e-mail is intended only for the person to whom it is
>>> > addressed. If you believe this e-mail was sent to you in error and the
>>> > e-mail
>>> > contains patient information, please contact the Partners Compliance
>>> > HelpLine at
>>> > http://www.partners.org/complianceline . If the e-mail was sent to you in
>>> > error
>>> > but does not contain patient information, please contact the sender and
>>> > properly
>>> > dispose of the e-mail.
>>> >
>>> 
>>> 
>>> ------------------------------
>>> 
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>> 
>>> End of Mne_analysis Digest, Vol 97, Issue 4
>>> *******************************************
> 
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160213/c097a9d9/attachment.html