<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
Hi Philip,
<div class=""><br class="">
</div>
<div class="">I think it makes sense to discuss this issue on the mailing list.</div>
<div class=""><br class="">
</div>
<div class="">The difference that you describe arise from the fact that the subject individual headmodels are NOT a spatially warped version of the template grid. The individual models were constructed from the individual subjects’ anatomical images. If it
is the intention to perform a source analysis on the cortical surface level, it’s always preferred (if possible) to use the subject-specific meshes, and not a spatially warped (i.e. warped by means of spatial transformations that are applicable to 3D volumetric
objects) template. This is because the gyrification is of course highly individual.</div>
<div class=""><br class="">
</div>
<div class="">Best wishes,</div>
<div class=""><br class="">
</div>
<div class="">Jan-Mathijd</div>
<div class=""><br class="">
</div>
<div class="">
<div>
<blockquote type="cite" class="">
<div class="">Begin forwarded message:</div>
<br class="Apple-interchange-newline">
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class="">
<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">From:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">Philip Cho <<a href="mailto:philip.cho@duke.edu" class="">philip.cho@duke.edu</a>><br class="">
</span></div>
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class="">
<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Subject:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">MOUS dataset source and head models</b><br class="">
</span></div>
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class="">
<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Date:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">9 November 2021 at 22:20:39 CET<br class="">
</span></div>
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class="">
<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">To:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">"<a href="mailto:jan.schoffelen@donders.ru.nl" class="">jan.schoffelen@donders.ru.nl</a>" <<a href="mailto:jan.schoffelen@donders.ru.nl" class="">jan.schoffelen@donders.ru.nl</a>><br class="">
</span></div>
<br class="">
<div class="">
<div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">
Hi Jan-Mathijs,</div>
<div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">
<br class="">
</div>
<div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">
I hope you're doing well. I once emailed you a long time ago about obtaining source and head models for LCMV on the MOUS dataset, and you kindly provided them. I've done a lot of work with source-level analysis since then, and the approach I've generally used
is to use the 8196-vertex template mesh defined in MNI space and warping it to subject space using the subject's MRI. I was using this approach in order to average these results across subjects. However, recently I have found that the warped meshes look slightly
different from the source models that you have provided. I assumed that they would be more spatially similar. In particular, the warped mesh seems to be more constricted (smaller) and pushed slightly farther back. In comparison, the source model that was provided
has points that push farther forward towards the front of the head volume. I'm curious why these differences arise? I have looked into it for some time now with little success, and I think it would help me going forward to understand this. I have attached
my warping code below. </div>
<div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">
<br class="">
</div>
<div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">
Thank you so much!</div>
<div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">
<br class="">
</div>
<div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">
Best,</div>
<div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">
Philip</div>
<div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">
<br class="">
</div>
<div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">
cd(['D:\MOUS\data\sub-' sub{1} '\anat']);
<div class=""> load([sub{1} 'vol.mat']);</div>
<div class=""> mri = ft_read_mri(['sub-' sub{1} '_space-CTF_T1w.nii']);</div>
<div class=""> mri.coordsys = 'ctf';</div>
<div class=""> <span class="Apple-converted-space"> </span></div>
<div class=""> % create the subject specific grid, using the template grid that has just been created</div>
<div class=""> cfg = [];</div>
<div class=""> cfg.method = 'basedonmni';</div>
<div class=""> cfg.template = template_grid;</div>
<div class=""> cfg.nonlinear = 'yes';</div>
<div class=""> cfg.mri = mri;</div>
<div class=""> cfg.unit ='mm';</div>
<div class=""> sourcemodel_warpedTemplate = ft_prepare_sourcemodel(cfg);</div>
<div class=""> save(['sourcemodel_warpedTemplate_surface8196_' sub{1} '.mat'],'sourcemodel_warpedTemplate');</div>
<div class=""><br class="">
</div>
<div class=""> % make a figure of the single subject headmodel, and grid positions</div>
<div class=""> figure; hold on;</div>
<div class=""> ft_plot_headmodel(vol, 'edgecolor', 'brain', 'facealpha', 0.4);</div>
<div class=""> ft_plot_mesh(sourcemodel_warpedTemplate.pos(sourcemodel_warpedTemplate.inside,:));</div>
<div class=""> savefig(gcf,['warpedsourceSurface8196_head_overlay_' sub{1} '.fig']);</div>
close all<br class="">
</div>
<div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">
<br class="">
</div>
<div style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">
<img size="801454" contenttype="image/png" data-outlook-trace="F:1|T:1" style="" class="" apple-inline="yes" id="AF83227F-A914-4060-ADF6-EB92D21DA511" src="cid:f30defd1-889d-47c1-9207-b3b34e3b36f0"><img size="800701" contenttype="image/png" data-outlook-trace="F:1|T:1" style="" class="" apple-inline="yes" id="2487771A-1461-4288-91C7-21773DDC2D67" src="cid:1989d850-f968-4230-998c-6ada8e1ebcea"></div>
</div>
</blockquote>
</div>
<br class="">
</div>
</body>
</html>