[FieldTrip] Error after MNE

[jan-mathijs schoffelen]

I don't know: did you follow up on bugzilla bug 2419? As mentioned in my earlier mail, for the time being you can work around it by commenting out line 421 in your local version of ft_read_headshape.

Jan-Mathijs




On Jan 7, 2014, at 7:12 PM, Nicholas Heugel wrote:

> Do you know if there is any update on the bug I encountered?  Does it look like an issue with setting up the analysis or is it an actual bug in the code?  Thanks for your assistance.
> 
> Nicholas
> 
> 
> On Wed, Dec 11, 2013 at 7:42 PM, Nicholas Heugel <nheugel89 at gmail.com> wrote:
> I did as you asked.  I put it in the core category with the error as the title
> 
> 
> On Wed, Dec 11, 2013 at 2:04 AM, jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl> wrote:
> Hi Nicholas,
> 
> It seems that the fif files lacks some information that FieldTrip assumes to be present. I would say that this can only be caused by the fact that the version of mne_make_source_space you used does not write the triangle area information into the fif file. Could you go to bugzilla.fcdonders.nl, create yourself an account, and file the issue as a bug? Please then also upload the fif-file you mentioned. I'll have a look at it and make the ft_read_headshape function more robust. In the mean time you could comment out line 421. 
> 
> Best,
> Jan-Mathijs
> 
> 
> 
> On Dec 10, 2013, at 6:23 PM, Nicholas Heugel wrote:
> 
>> I a trying to go through the tutorial for the 
>> Source reconstruction of event-related fields using minimum-norm estimate
>> 
>> I am able to run everything up to the MNE with no problem, and it seems like the MNE portion works.  But when I run the command bnd = ft_read_headshape('Subject01-oct-6-src.fif', 'format', 'mne_source');
>> and then plot it to visualize the source space.  I get the error Reference to non-existent field 'use_tri_area'. Error in ft_read_headshape (line 421) shape.area = [src(1).use_tri_area(:); src(2).use_tri_area(:)];
>>  I have looked on this site and online and can't find an explanation of what is wrong or how to fix the problem.  Any help would be appreciated.  I am using an Anatomical MRI scan for the head model analysis, the skull is present and I manually am Identifying the fiducials.    Also, a few steps earlier it had me check the white matter segmentation done by Freesurfer and that worked fine and what I get closely resembles the tutorial.  So I think the problem is somewhere in the MNE I am just not sure where.  Any help would be appreciated.  Thank you for your time.
>> Nicholas
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> 
> Jan-Mathijs Schoffelen, MD PhD 
> 
> Donders Institute for Brain, Cognition and Behaviour, 
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> 
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
> 
> J.Schoffelen at donders.ru.nl
> Telephone: +31-24-3614793
> 
> http://www.hettaligebrein.nl
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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