[Mne_analysis] mne_analyze surface viewer error

[Vincent Rupp]

Using the -gcatlas option with mne_watershed_bem successfully resolved this
issue; thanks for the helpful responses. Also, I just wanted to suggest
packaging libgfortran.so.1 with new MNE installations because it seems to
cause issues with many users who have newer versions of the library already
installed. Thanks again!


Best wishes,

Vincent Rupp


On Tue, Feb 5, 2013 at 1:48 PM, Vincent Rupp <rupp.vincent at gmail.com> wrote:

> Thanks all for the great responses. I had already checked the T1 and
> surfaces, and so that was why the blockhead was confusing. I will follow up
> with Matti's advice and try the nightly builds and re-run the BEM
> generation. Three out of approx 34 subjects had similar issues, so we'll
> see if the nightly build new BEM mesh takes care of them. Thanks again.
>
>
> Best wishes,
>
> Vincent Rupp
>
>
> On Tue, Feb 5, 2013 at 4:54 AM, Matti Hamalainen <msh at nmr.mgh.harvard.edu>wrote:
>
>>
>> Hello,
>>
>> The BEM surface segmentation using mne_watershed_bem has gone wrong.
>> There is most probably a way the avoid this. There are new options
>> --gcatlas and --preflood <number> for mne_watershed_bem in the nightly
>> build.
>> I do not recall which one of them helps, I hope someone at the Martinos
>> can help you.
>>
>> - Matti
>>
>> On Feb 4, 2013, at 7:55 PM, Vincent Rupp wrote:
>>
>> Hello,
>>
>> I am using mne_analyze to align MEG/MRI coordinates in accordance with
>> the instructions at
>> http://www.martinos.org/mne/manual/sampledata.html#chdijbig. However I
>> am having an issue with some of the way my inflated surfaces appear when
>> displayed in the viewer. I've attached two examples of some particularly
>> bad ones, and the third attachment is an example of what the inflated
>> surface looks like ordinarily. This third image is the same surface as the
>> first one that looks like a block. At what point in processing is my
>> workflow going wrong? Thanks in advance.
>>
>> Best wishes,
>>
>> Vincent Rupp
>>  <Screenshot from 2013-02-04 16:47:26.png><Screenshot from 2013-02-04
>> 16:49:20.png><Screenshot from 2013-02-04 16:48:24.png>
>> _______________________________________________
>>
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>>
>>
>>    ---------
>>
>> Matti Hamalainen, Ph.D.
>> Athinoula A. Martinos Center for Biomedical Imaging
>> Massachusetts General Hospital
>>
>> msh at nmr.mgh.harvard.edu
>> mhamalainen at partners.org
>>
>>
>>
>>
>>
>>
>> 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.
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20130211/aa4a303c/attachment.html