[FieldTrip] Editing Vertices of Scalp Manually or Automatically

[jan-mathijs schoffelen]

Isaiah,

Image segmentation algorithms work by thresholding an image (which has optionally been subjected to a sequence of image processing steps) at a sensible threshold, creating a binary image (i.e. consisting only of 0 and 1s). Then, in order to generate a surface description of e.g. the scalp, a triangulation is created that describes the boundary from 0 to 1, assuming the voxels with a value of 1 to lie within a single compartment. In your scalp mesh, the ‘horns’ are most likely caused by voxels with a supra threshold intensity value. After thresholding, the binary volume consists of multiple disconnected ‘blobs’, and the triangulation algorithm connects the points at the boundaries of these individual islands.  Thus, in your case, the default image processing steps (which actually aim at generating a single compartment (by keeping the largest connected compartment, and throwing away the smaller islands) have failed. This may be caused by the fact that these islands lie at the edge of your image. If you don’t feel comfortable with editing the volumetric image yourself I suggest that you play with the cfg.scalpsmooth and cfg.scalpthreshold parameters prior to calling ft_volumesegment. I would start by increasing the scalpthreshold (the default value is 0.1, but you can try 0.3, or 0.5, or any value you fancy).
Finally, please note that everybody who spends his/her valuable time on answering questions on this discussion list is doing so on a voluntary basis. Be aware that multiple postings of the same question does not necessary enhance people’s inclination to answer, although I realize fully well that it may be frustrating if you are stuck.

Best wishes,
Jan-Mathijs

On Jul 15, 2014, at 12:47 AM, Isaiah C. Smith <Isaiah.C.Smith.17 at dartmouth.edu> wrote:

> Thanks Arjen, 
> 
> I was able to bring up the source plot of the the scalp using:
> >> cfg.funparameter=‘scalp';
> >> ft_sourceplot(cfg,segmentedmri)
> Results:
> <Screen Shot 2014-07-14 at 3.44.14 PM.png>
> Could you please explain how to create/adjust the inclusion threshold? Sorry, I am a little new to the fieldtrip functions.
> 
> Isaiah 
> 
> On Jul 14, 2014, at 2:46 PM, Stolk, A. (Arjen) <a.stolk at fcdonders.ru.nl> wrote:
> 
>> Hi Isaiah,
>> 
>> It could be that your problem is caused by your structural scan containing voxels outside the head but with levels of intensity falling in the range of that attributed to, say, csf. One way to check is by plotting the respective segmented brain mask, e.g. 
>> 
>> mri.pow = seg.csf
>> cfg.funparameter = 'pow'
>> ft_sourceplot(cfg,mri)
>> 
>> You could then try and manually include certain voxels by playing with the inclusion threshold (e.g. set seg.csf with voxelvalues smaller than .99 to 0). This would allow to work around that problem, unless those voxels have exactly the same intensity as csf.
>> 
>> Hope this helps narrowing the origin of your problem,
>> Arjen
>> 
>> 
>> 
>> Van: "Isaiah C. Smith" <Isaiah.C.Smith.17 at dartmouth.edu>
>> Aan: fieldtrip at science.ru.nl
>> Verzonden: Maandag 14 juli 2014 23:28:59
>> Onderwerp: [FieldTrip] Editing Vertices of Scalp Manually or Automatically
>> 
>> Hello Everyone,
>> 
>> I am having a problem with noise appearing in my volume conduction model. There are a few horn-like images on the head, and a cluster of vertices in the area where a neck would normally appear but the MRI was only of the upper half of someone's head so it should not be appearing either. I am running into a wall when I try to edit manually because the data so large I cannot view it. Please, I have been trying to fix this for a while does anyone have any ideas on how to get rid of these extraneous points: whether manually or by shifting parameters in the segmentation process? Your help would be extremely helpful and greatly appreciated.
>> 
>> This is an image of the problem described.
>> <Screen Shot 2014-07-14 at 2.21.48 PM.png>
>> 
>> Kind Regards,
>> 
>> Isaiah
>> 
>> ***************************
>> Isaiah Smith ( Dartmouth Undergraduate)
>> UCLA California NanoSystems Institute Summer Intern
>> University of California Los Angeles
>> Dr. Wentai Liu’s Biomimetics Lab
>> Rm 5311
>> 
>> 
>> 
>> 
>> _______________________________________________
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>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> 
>> 
>> 
>> -- 
>> Donders Institute for Brain, Cognition and Behaviour
>> Centre for Cognitive Neuroimaging
>> Radboud University Nijmegen
>> 
>> Email:  a.stolk at donders.ru.nl
>> Phone:  +31(0)243 68294
>> Web:    www.arjenstolk.nl
>> _______________________________________________
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> 
> _______________________________________________
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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

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