<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Isaiah,<div><br></div><div>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).</div><div>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.</div><div><br></div><div>Best wishes,</div><div>Jan-Mathijs</div><div><br></div><div>On Jul 15, 2014, at 12:47 AM, Isaiah C. Smith <<a href="mailto:Isaiah.C.Smith.17@dartmouth.edu">Isaiah.C.Smith.17@dartmouth.edu</a>> wrote:</div><div><div><br class="Apple-interchange-newline"><blockquote type="cite">
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Thanks Arjen,
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<div>I was able to bring up the source plot of the the scalp using:</div>
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<div>>> cfg.funparameter=‘scalp';</div>
<div>>> ft_sourceplot(cfg,segmentedmri)</div>
<div>Results:</div>
<div><span><Screen Shot 2014-07-14 at 3.44.14 PM.png></span></div>
<div>Could you please explain how to create/adjust the inclusion threshold? Sorry, I am a little new to the fieldtrip functions.</div>
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<div>Isaiah </div>
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<div>On Jul 14, 2014, at 2:46 PM, Stolk, A. (Arjen) <<a href="mailto:a.stolk@fcdonders.ru.nl">a.stolk@fcdonders.ru.nl</a>> wrote:</div>
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<div style="font-family: 'Times New Roman'; font-size: 12pt;">Hi Isaiah,<br>
<br>
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.<span class="Apple-converted-space"> </span><br>
<br>
mri.pow = seg.csf<br>
cfg.funparameter = 'pow'<br>
ft_sourceplot(cfg,mri)<br>
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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.<br>
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Hope this helps narrowing the origin of your problem,<br>
Arjen<br>
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<blockquote style="border-left-width: 2px; border-left-style: solid; border-left-color: rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;">
<b>Van:<span class="Apple-converted-space"> </span></b>"Isaiah C. Smith" <<a href="mailto:Isaiah.C.Smith.17@dartmouth.edu">Isaiah.C.Smith.17@dartmouth.edu</a>><br>
<b>Aan:<span class="Apple-converted-space"> </span></b><a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>
<b>Verzonden:<span class="Apple-converted-space"> </span></b>Maandag 14 juli 2014 23:28:59<br>
<b>Onderwerp:<span class="Apple-converted-space"> </span></b>[FieldTrip] Editing Vertices of Scalp Manually or Automatically<br>
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Hello Everyone,
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<div>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.</div>
<div><br>
</div>
<div>This is an image of the problem described.</div>
<div><span><Screen Shot 2014-07-14 at 2.21.48 PM.png></span></div>
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<div>Kind Regards,</div>
<div><br>
</div>
<div>Isaiah</div>
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<div>***************************</div>
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<div style="font-family: Tahoma; font-size: 13px; background-color: rgb(255, 255, 255);">
<font face="Arial"><i>Isaiah Smith ( Dartmouth Undergraduate)</i></font></div>
<div style="font-family: Tahoma; font-size: 13px; background-color: rgb(255, 255, 255);">
<i style="font-family: Arial;">UCLA California NanoSystems Institute Summer Intern</i></div>
<div style="font-family: Tahoma; font-size: 13px; background-color: rgb(255, 255, 255);">
<i style="font-family: Arial;">University of California Los Angeles</i></div>
<div style="background-color: rgb(255, 255, 255);"><i><font face="Arial" size="2">Dr. Wentai Liu’s Biomimetics Lab</font></i></div>
<div style="font-family: Tahoma; font-size: 13px; background-color: rgb(255, 255, 255);">
<i style="font-family: Arial;">Rm 5311</i></div>
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<div><span name="x"></span>Donders Institute for Brain, Cognition and Behaviour<br>
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color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Jan-Mathijs Schoffelen, MD PhD </div><div><br></div><div>Donders Institute for Brain, Cognition and Behaviour, <br>Centre for Cognitive Neuroimaging,<br>Radboud University Nijmegen, The Netherlands</div><div><br></div><div>Max Planck Institute for Psycholinguistics,</div><div>Nijmegen, The Netherlands</div><div><br></div><div><a href="mailto:J.Schoffelen@donders.ru.nl">J.Schoffelen@donders.ru.nl</a></div><div>Telephone: +31-24-3614793</div><div><br></div><div><a href="http://www.hettaligebrein.nl">http://www.hettaligebrein.nl</a></div></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></span>
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