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<p>Dear Sarah,<o:p></o:p></p>
<p>I would first recommend verifying that the coordinate systems and units of your atlas and template MRI are consistent. However, this does not appear to be the issue in your case.<o:p></o:p></p>
<p>The likely cause of the discrepancy is that out of the <span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">
6871 </span>dipoles marked as “inside” the brain , there are regions such as the brain ventricles and the brainstem. These regions are not part of the 116 AAL ROIs, as depicted in Figure 2 of
<a href="https://www.researchgate.net/publication/350967572_A_Deep_Learning_Approach_to_Predict_Autism_Spectrum_Disorder_Using_Multisite_Resting-State_fMRI" target="_new">
this paper</a> (<a href="https://www.researchgate.net/publication/350967572_A_Deep_Learning_Approach_to_Predict_Autism_Spectrum_Disorder_Using_Multisite_Resting-State_fMRI">https://www.researchgate.net/publication/350967572_A_Deep_Learning_Approach_to_Predict_Autism_Spectrum_Disorder_Using_Multisite_Resting-State_fMRI</a>).
Furthermore, your 7.5 mm source model is relatively coarse, and the boundary between "inside" and "outside" is not well-defined, leading to points that are “inside” the brain not assigned to any AAL ROI.<o:p></o:p></p>
<p>To visualize this better, you can plot the atlas-interpolated source model using the following code:<o:p></o:p></p>
<pre><code>cfg = [];<o:p></o:p></code></pre>
<pre><code>cfg.funparameter = 'tissue';<o:p></o:p></code></pre>
<pre><code>cfg.funcolormap = 'jet';<o:p></o:p></code></pre>
<pre><code>ft_sourceplot(cfg, sourcemodel2);<o:p></o:p></code></pre>
<p>Additionally, by specifying <code><span style="font-size:10.0pt">cfg.method = 'surface';</span></code>, you can check the brain surface. You will observe that some boundary points are not assigned to any AAL ROI (e.g., note the dark blue spots on the occipital
lobe):<o:p></o:p></p>
<pre><code>cfg = [];<o:p></o:p></code></pre>
<pre><code>cfg.method = 'surface';<o:p></o:p></code></pre>
<pre><code>cfg.funparameter = 'tissue';<o:p></o:p></code></pre>
<pre><code>cfg.funcolormap = 'jet';<o:p></o:p></code></pre>
<pre><code>ft_sourceplot(cfg, sourcemodel2);<o:p></o:p></code></pre>
<p><o:p> </o:p></p>
<p>Best regards,<o:p></o:p></p>
<p>Konstantinos Tsilimparis<o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:Consolas"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> fieldtrip <fieldtrip-bounces@science.ru.nl>
<b>On Behalf Of </b>Sarah via fieldtrip<br>
<b>Sent:</b> Wednesday, July 3, 2024 11:13 PM<br>
<b>To:</b> fieldtrip@science.ru.nl<br>
<b>Cc:</b> Sarah <s83728498@gmail.com><br>
<b>Subject:</b> [FieldTrip] Source Point Count & Atlas Point Count Discrepancy<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="gmail-p1" style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">Hi all, <o:p></o:p></span></p>
<p class="gmail-p2" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;min-height:15px">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"><o:p> </o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">I have a question about mapping source points to atlas ROIs.<span class="gmail-apple-converted-space"> </span><o:p></o:p></span></p>
<p class="gmail-p2" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;min-height:15px">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"><o:p> </o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">I have computed my source analysis using FT’s 3D grid of 7.5mm. I have also interpolated the FT shipped AAL atlas (ROI_MNI_V4.nii) onto this 7.5mm template grid.<o:p></o:p></span></p>
<p class="gmail-p2" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;min-height:15px">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"><o:p> </o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">I have now been mapping only some relevant source points to the atlas to determine which ROI they exist in. However, I noticed that many of my source points didn’t “exist” within the atlas. In
fact, the # of my subject’s source points that exist inside/outside are reported as: 6871 dipoles inside, 6791 dipoles outside brain, whereas I notice the atlas interpolated source model only has 3475 points total.<span class="gmail-apple-converted-space"> </span><o:p></o:p></span></p>
<p class="gmail-p2" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;min-height:15px">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"><o:p> </o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">I was wondering how to handle this apparent discrepancy (as I assume the atlas point count should at least be somewhat closer to the total of source points marked as inside the brain).<span class="gmail-apple-converted-space"> </span><o:p></o:p></span></p>
<p class="gmail-p2" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;min-height:15px">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"><o:p> </o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">Thanks,<o:p></o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">Sarah<o:p></o:p></span></p>
<p class="gmail-p2" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;min-height:15px">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"><o:p> </o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">P.S. I included some of my relevant code below to produce this, but it is simply the code of the FT tutorials.<o:p></o:p></span></p>
<p class="gmail-p2" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;min-height:15px">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"><o:p> </o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">Subject Sourcemodel Code:<o:p></o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg <span class="gmail-apple-converted-space">
</span>= [];<o:p></o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg.method<span class="gmail-apple-converted-space">
</span>='basedonmni';<o:p></o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg.template<span class="gmail-apple-converted-space">
</span>= template_grid;<o:p></o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg.nonlinear = 'yes';<o:p></o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg.mri <span class="gmail-apple-converted-space">
</span>= mri;<o:p></o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg.unit<span class="gmail-apple-converted-space">
</span>='mm';<o:p></o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">grid<span class="gmail-apple-converted-space">
</span>= ft_prepare_sourcemodel(cfg);<o:p></o:p></span></p>
<p class="gmail-p2" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;min-height:15px">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"><o:p> </o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">Interpolate Atlas Code:<span class="gmail-apple-converted-space"> </span><o:p></o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg = [];<o:p></o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg.interpmethod = 'nearest';<o:p></o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg.parameter = 'tissue';<o:p></o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">sourcemodel2 = ft_sourceinterpolate(cfg, atlas, template_grid);<o:p></o:p></span></p>
<p class="gmail-p1" style="margin:0cm;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal">
<span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">sourcemodel2 = ft_convert_units(sourcemodel2, 'mm');<o:p></o:p></span></p>
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