[FieldTrip] Editing Vertices of Scalp Manually or Automatically

Isaiah C. Smith Isaiah.C.Smith.17 at dartmouth.edu
Wed Jul 16 00:13:13 CEST 2014


[cid:6DCD99BF-1FEB-4B85-90B8-E1368132E32C at host.ucla.edu]On

I should probably show you the MRI as well. The reason as to why I am so confused is that there are no points below and still the neck-like image shows up. I cannot find any variation in intensity at all. Is there any explanation for this occurrence? Thanks once again.

Isaiah

 Jul 15, 2014, at 2:57 PM, Isaiah C. Smith <Isaiah.C.Smith.17 at dartmouth.edu<mailto:Isaiah.C.Smith.17 at dartmouth.edu>> wrote:

Thank you so much for your reply Arjen,

I was wondering if there is there any solution in the interface where we can automatically exclude some unwanted point? In the segmentation process? Or in a later process?  When I change the threshold I get an error message concerning the final steps in creating the head model.

Isaiah Smith
On Jul 14, 2014, at 2:46 PM, Stolk, A. (Arjen) <a.stolk at fcdonders.ru.nl<mailto: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<mailto:Isaiah.C.Smith.17 at dartmouth.edu>>
Aan: fieldtrip at science.ru.nl<mailto: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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--
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen

Email:  a.stolk at donders.ru.nl<mailto:a.stolk at donders.ru.nl>
Phone:  +31(0)243 68294
Web:    www.arjenstolk.nl<http://www.arjenstolk.nl/>
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