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Hi Philip,
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</div>
<div class="">I am posting my answer here to the fieldtrip list (again), so that more people might benefit from the discussion, and/or will be given the opportunity to chime in, should they feel inclined. </div>
<div class=""><br class="">
</div>
<div class="">Given that you are probably using a ’singleshell’ method for the forward model computation, the easiest would be to explicitly state that all dipoles are ‘inside’ prior to the source reconstruction. Unlike BEM forward models, a slight mismatch
between the singleshell boundary and the dipole positions is not too worrisome.</div>
<div class="">You can achieve this by specifying sourcemodel.inside = true(size(sourcemodel.pos,1),1); prior to computing the forward model / inverse model. If the inside vector is not specified, FT will create one by comparing the boundary of the volume conductor
model with the dipole positions, causing the dipoles that ’stick out’ (which is the consequence of using slightly different pipelines and softwares for the sourcemodel vs. volume conductor model creation) to be classified as outside.</div>
<div class=""><br class="">
</div>
<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
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</div>
<div class=""><br class="">
</div>
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<div><br class="">
<blockquote type="cite" class="">
<div class="">On 11 Jan 2022, at 09:05, Philip Cho <<a href="mailto:philip.cho@duke.edu" class="">philip.cho@duke.edu</a>> wrote:</div>
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Hi Jan Mathijs,</div>
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Thank you so much for your extremely detailed response. I now have a very good understanding of how this all works spatially. Peculiarly, the 8196-node template from the Fieldtrip distribution does not seem to be in the same topological space as the MOUS subjects,
but I was given an atlas with parcellations, which seems to contain the topologically equivalent surface that I'm looking for. I've been using that, and it seems successful. The only issue I seem to now have is that there are a few subjects where one node
is just outside the head model, and as such, timecourses are not calculated at those points for that given subject. While this has negligible effects on my analyses for individual subjects, it seems to create some problems when I'm trying to use something
like ft_sourcegrandaverage , which expects there to be a timecourse for every subject at a given point. If a point has a timecourse for every subject except one, I get an error for inconsistent array sizes, and I'm not able to obtain an average. Of course,
I can try to average manually, but I would prefer to stay consistent and use FieldTrip functions throughout. If you know a quick way around this, please do let me know. Otherwise, I will proceed with a manual approach. Thank you again!</div>
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Best,</div>
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Philip</div>
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<font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:janmathijs.schoffelen@donders.ru.nl" class="">janmathijs.schoffelen@donders.ru.nl</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Monday, January 3, 2022 4:49 AM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Philip Cho <<a href="mailto:philip.cho@duke.edu" class="">philip.cho@duke.edu</a>><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: MOUS dataset source and head models</font>
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Hi Philip,
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</div>
<div class="">When thinking about surface meshes, there are 2 things to take into account:</div>
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<div class="">1) the positions of the vertices, and</div>
<div class="">2) the way the vertices are connected (i.e. the edges), which is typically defined in terms of the triangles.</div>
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</div>
<div class="">As long as the set of vertices is well-defined, i.e. each one of them is defined in relation to the other one (e.g. by giving them a unique index number, ranging from 1 to, say, 8196), the absolute position of the vertices can be played with.
Also, importantly, as long as a 8196-node cortical surface is topologically equivalent to another 8196-node (note that this is not a given) surface, a parcellation scheme (e.g. atlas) defined on one surface can be directly applied to the other one (see below).</div>
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</div>
<div class="">Of course, in real life situations, the positions of the set of vertices are defined in some coordinate system that relates to a realistic anatomical shape, but for the template registration this is actually irrelevant (and nor is it for the visualization).
For this reason, often surface-based results are displayed on an ‘inflated’ cortical surface, to allow for looking into the sulci. Thus, the - what you refer to as template - cortical surface that you attached to your previous message is an inflated cortical
surface, that is by definition not defined in any real-world coordinate system.</div>
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</div>
<div class="">Surface based template matching takes place in topological space, where the subjects’ hemisphere specific meshes, which are topological spheres, are matched to a spherical template. This spherical template has the most important cortical landmarks
defined, to which the individual surfaces are morphed. These landmarks are fissures/sulci etc. This registration procedure is fundamentally different from a volume based registration procedure.</div>
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</div>
<div class="">Now, I am not 100% sure that the 8196 node template in the fieldtrip distribution is in the same topological space as the topological space used for the MOUS subjects, but it could be the case (I am pretty sure it is). The reason I mention it,
is that you give the impression that you’d like to define ROIs in MNI space, and use the fieldtrip template to identify the relevant vertex indices, in order to transport those indices to the data from MOUS. In general, I would discourage people to combine
surface-based source models with ROIs (or atlases) defined in volumetric space, but it’s of course not forbidden. Should you want to walk that path, you indeed need to ensure that the vertex positions of template surface are in a well-defined coordinate space.</div>
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<div class="">To verify this, you may need to visualize the cortical mesh in an overlay on top of an anatomical image that is in the desired coordinate space.</div>
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</div>
<div class="">I quickly checked to verify that the surface mesh in FT surf = ft_read_headshape('cortex_8196.surf.gii’);</div>
<div class="">is in register with the anatomical template: mri = ft_read_mri(’single_subj_T1_1mm.nii’);</div>
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</div>
<div class="">figure;ft_plot_ortho(mri.anatomy,’transform’,mri.transform,’intersectmesh’,surf);</div>
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</div>
<div class="">Provided the template anatomy is in standardized space, and the surface mesh is in topological register with the ones used for MOUS, you should be good to go.</div>
<div class=""><br class="">
</div>
<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
<div class=""><br class="">
</div>
<div class=""><span id="cid:D04A8CC9-5D25-4AFC-8849-1225780A5C90"><Screenshot 2022-01-03 at 10.49.13.png></span></div>
<div class=""><br class="">
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<div class="">
<div class="">,<br class="">
<blockquote type="cite" class="">
<div class="">On 2 Jan 2022, at 08:50, Philip Cho <<a href="mailto:philip.cho@duke.edu" class="">philip.cho@duke.edu</a>> wrote:</div>
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The question I just asked with respect to the warping is of interest to me, but I'm now putting together that it's not very relevant. The part that I had missed was that the dipole positions for individual-subject meshes are already comparable across subjects,
since they supposedly are surface registered to a common template. That being said, I'm slightly confused now as to which template this is. The dipole position indices from the individual meshes (provided from your group) do not seem to correspond to the 8196-<span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">vertex
template provided with FieldTrip, but instead, they correspond to the indices in "cortex_inflated_8196reg.mat", which is provided with the dataset. Is this correct? The template from FieldTrip is expressed in MNI coordinates, so it was easy to apply ROIs and
such, but I'm noticing that the other template (supposedly the correct one) is more ambiguous, given that it's shifted to the left, as depicted below. If it could be clarified if this is the correct template, and if so, what coordinate system it's in, I think
this would be the last bit of help I would need. Thank you so much so far! My understanding has improved tremendously. </span></div>
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<font face="Calibri, sans-serif" class="" style="font-size: 11pt;"><b class="">From:</b><span class="x_Apple-converted-space"> </span>Philip Cho <<a href="mailto:philip.cho@duke.edu" class="">philip.cho@duke.edu</a>><br class="">
<b class="">Sent:</b><span class="x_Apple-converted-space"> </span>Sunday, January 2, 2022 1:28 AM<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span>Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:janmathijs.schoffelen@donders.ru.nl" class="">janmathijs.schoffelen@donders.ru.nl</a>><br class="">
<b class="">Subject:</b><span class="x_Apple-converted-space"> </span>Re: MOUS dataset source and head models</font>
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Hi Jan-Mathijs,</div>
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Thanks so much for your response. I am subscribed to the discussion list and regularly receive email notifications, but I was never able to see your original response, and I still cannot seem to find it. Regardless, I really apologize that you had to answer
my question twice. With regard to your response, I understand that the warped template won't exactly match the individual-subject meshes, but I thought the general size/outline of the two meshes would be more similar, given that the template was warped based
on the individual subject's MRI. The warping seems to orient the brain correctly, but the shape/size of the mesh remains vastly different, which makes me think the warping did not work completely as intended. Please let me know if there's something I'm still
not understanding here. Thank you so much!</div>
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Best,</div>
<div class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
Philip</div>
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<div id="x_x_divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" class="" style="font-size: 11pt;"><b class="">From:</b><span class="x_Apple-converted-space"> </span>Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:janmathijs.schoffelen@donders.ru.nl" class="">janmathijs.schoffelen@donders.ru.nl</a>><br class="">
<b class="">Sent:</b><span class="x_Apple-converted-space"> </span>Tuesday, December 28, 2021 3:59 AM<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span>Philip Cho <<a href="mailto:philip.cho@duke.edu" class="">philip.cho@duke.edu</a>><br class="">
<b class="">Subject:</b><span class="x_Apple-converted-space"> </span>Re: MOUS dataset source and head models</font>
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<div class="" style="word-wrap: break-word; line-break: after-white-space;">Hi Philip,
<div class=""><br class="">
</div>
<div class="">If I recall well, I have already answered to the e-mail you copied in below. I forwarded it to the discussion list, and answered it there. If you haven’t received that answer, then I strongly suggest you to subscribe to the discussion list. If
you received the answere, then I don’t know what there is to add. In that case you need to formulate your question in a different way, because then I don’t understand what the problem is.</div>
<div class=""><br class="">
</div>
<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
<div class=""><br class="">
<div class=""><br class="">
</div>
<div class=""><span class="">Hi Philip,</span>
<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>
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On 28 Dec 2021, at 08:32, Philip Cho <<a href="mailto:philip.cho@duke.edu" class="">philip.cho@duke.edu</a>> wrote:</div>
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Hi Jan-Mathijs,</div>
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I apologize if this is not the most appropriate way to contact you, but I've worked at this issue for some time now and still don't quite understand what the issue is. It's quite critical that I get this part right, so I hope it's understandable that I'm reaching
out for your input. Any help would be appreciated. Thank you so much! </div>
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Best,</div>
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Philip</div>
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<span class="x_Apple-converted-space"> </span><span class="" style="font-family: Helvetica; font-size: 14px; 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; text-decoration: none; float: none; display: inline !important;"></span><span class="x_Apple-converted-space"> </span>
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<font face="Calibri, sans-serif" class="" style="font-size: 11pt;"><b class="">From:</b><span class="x_x_x_Apple-converted-space"> </span>Philip Cho<br class="">
<b class="">Sent:</b><span class="x_x_x_Apple-converted-space"> </span>Tuesday, November 9, 2021 4:20 PM<br class="">
<b class="">To:</b><span class="x_x_x_Apple-converted-space"> </span><a href="mailto:jan.schoffelen@donders.ru.nl" class="">jan.schoffelen@donders.ru.nl</a><span class="x_x_x_Apple-converted-space"> </span><<a href="mailto:jan.schoffelen@donders.ru.nl" class="">jan.schoffelen@donders.ru.nl</a>><br class="">
<b class="">Subject:</b><span class="x_x_x_Apple-converted-space"> </span>MOUS dataset source and head models</font>
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<div class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
Hi Jan-Mathijs,</div>
<div class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">
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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>
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Thank you so much!</div>
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Best,</div>
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Philip</div>
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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="x_x_x_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>
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<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="">
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