<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Thomas,<div class=""><br class=""></div><div class="">unfortunately I cannot see the figure you send. But from the title of the email I think i have some suggestions for you.</div><div class=""><br class=""></div><div class=""><blockquote type="cite" class=""><div dir="ltr" class=""><div class="">%volume conduction model<br class="">cfg = [];<br class="">cfg.output = {'brain', 'skull', 'scalp'};<br class="">mri_segmented = ft_volumesegment(cfg, mri_resliced);</div></div></blockquote></div><div class=""><br class=""></div><div class="">for this segment you can play around with to make the the tissues more smooth</div><div class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class="">% cfg.brainsmooth = 'no', or scalar, the FWHM of the gaussian kernel in voxels, (default = 5)</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class="">% cfg.scalpsmooth = 'no', or scalar, the FWHM of the gaussian kernel in voxels, (default = 5)</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class="">% cfg.skullsmooth = 'no', or scalar, the FWHM of the gaussian kernel in voxels, (default = 5)</div></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class=""><br class=""></div><div class="">Or you can change the thresholds for the tissues</div><div class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class="">% cfg.brainthreshold = 'no', or scalar, relative threshold value which is used to threshold the</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class="">% tpm in order to create a volumetric brainmask (see below), (default = 0.5)</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class="">% cfg.scalpthreshold = 'no', or scalar, relative threshold value which is used to threshold the</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class="">% anatomical data in order to create a volumetric scalpmask (see below),</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class="">% (default = 0.1)</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class="">% cfg.skullthreshold = 'no', or scalar, relative threshold value which is used to threshold the</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class="">% anatomical data in order to create a volumetric scalpmask (see below),</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class="">% (default = 0.5). this parameter is only used when</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class="">% the segmetnation contains 6 tissue types,</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class="">% including 'bone’,</div></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class=""><br class=""></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class=""><blockquote type="cite" style="font-family: Helvetica; font-size: 12px;" class=""><div dir="ltr" class=""><div class="">%reconstruct the three triangulated meshes.<br class="">cfg = [];<br class="">cfg.method = 'projectmesh';<br class="">cfg.tissue = 'brain';<br class="">cfg.numvertices = 3000;<br class="">mesh_eeg(1) = ft_prepare_mesh(cfg, mri_segmented);<br class=""><br class="">cfg.tissue = 'skull';<br class="">cfg.numvertices = 2000;<br class="">mesh_eeg(2) = ft_prepare_mesh(cfg, mri_segmented);<br class=""><br class="">cfg.tissue = 'scalp';<br class="">cfg.numvertices = 1000;<br class="">mesh_eeg(3) = ft_prepare_mesh(cfg, mri_segmented);</div></div></blockquote></div><div class=""><br class=""></div><div class="">If the previous steps to not solve your problems, you can also try to change something in the method</div><div class=""><div class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class="">% cfg.method = string, can be 'interactive', 'projectmesh', 'iso2mesh', 'isosurface',</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Courier; color: rgb(37, 153, 45);" class="">% 'headshape', 'hexahedral', 'tetrahedral', 'cortexhull'</div></div></div><div class=""><br class=""></div><div class="">Cheers,</div><div class=""><br class=""><div class="">
Simon Homölle<br class="">PhD Candidate<br class="">Donders Institute for Brain, Cognition and Behaviour<br class="">Centre for Cognitive Neuroimaging<br class="">Radboud University Nijmegen<br class="">Phone: +31-(0)24-36-65059
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<br class=""><div><blockquote type="cite" class=""><div class="">On 22 May 2018, at 00:53, Thomas Radman <<a href="mailto:radman.thomas@gmail.com" class="">radman.thomas@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div dir="ltr" class=""><div class="">Hello,</div><div class=""><br class=""></div><div class="">I am trying to segment an individual subject's MRI following this tutorial:</div><div class=""><a href="http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting" class="">http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting</a></div><div class=""><br class=""></div><div class="">However, when plotting the mesh of the scalp segmentation I get these horrible disfigurations that are not in the original MRI. Here is a screenshot:<br class=""></div><div class=""><br class=""></div><div class=""><img src="x-msg://6/?ui=2&ik=4c33b381d2&view=att&th=16384b2eb74a776e&attid=0.1&disp=safe&realattid=ii_jhgsh5pm0_16384b2eb74a776e&zw" width="416" height="294" class=""><br class=""></div><div class=""><br class=""></div><div class="">These are the steps I'm taking<br class=""></div><div class="">mri=ft_read_mri( '/data/radmantc/projects/T1_mni.nii')<br class="">mri.coordsys='mni'</div><div class=""><br class=""></div><div class="">cfg = [];<br class="">cfg.resolution = 1;<br class="">mri_resliced = ft_volumereslice(cfg, mri);<br class="">figure<br class="">ft_sourceplot([], mri_resliced);</div><div class=""><br class=""></div><div class="">%volume conduction model<br class="">cfg = [];<br class="">cfg.output = {'brain', 'skull', 'scalp'};<br class="">mri_segmented = ft_volumesegment(cfg, mri_resliced);<br class=""><br class="">% copy the anatomy into the segmented mri<br class="">mri_segmented.anatomy = mri_resliced.anatomy;<br class=""></div><div class=""><br class=""></div><div class="">%reconstruct the three triangulated meshes.<br class="">cfg = [];<br class="">cfg.method = 'projectmesh';<br class="">cfg.tissue = 'brain';<br class="">cfg.numvertices = 3000;<br class="">mesh_eeg(1) = ft_prepare_mesh(cfg, mri_segmented);<br class=""><br class="">cfg.tissue = 'skull';<br class="">cfg.numvertices = 2000;<br class="">mesh_eeg(2) = ft_prepare_mesh(cfg, mri_segmented);<br class=""><br class="">cfg.tissue = 'scalp';<br class="">cfg.numvertices = 1000;<br class="">mesh_eeg(3) = ft_prepare_mesh(cfg, mri_segmented);<br class=""><br class="">figure<br class="">ft_plot_mesh(mesh_eeg(1), 'edgecolor', 'none', 'facecolor', 'r')<br class="">ft_plot_mesh(mesh_eeg(2), 'edgecolor', 'none', 'facecolor', 'g')<br class="">ft_plot_mesh(mesh_eeg(3), 'edgecolor', 'none', 'facecolor', 'b') %this is the only mesh that is distorted<br class="">alpha 0.3<br class=""></div><div class=""><br class=""></div><div class="">Also, can someone tell me how to respond to any replies I might get. In previous posts, I only see the replies in the listserv digest emails. Do I create a new email with the subject line of this case intact? I don't get an email directly from the person sending the reply to my email, I only see it in the digest.<br class=""></div><div class=""><br class=""></div><div class="">Thank you for the help,</div><div class="">Thomas Radman<br class=""></div><div class=""><br class=""></div></div>
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