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<p class="MsoNormal">Hi Robert, <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you so much for the response! <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">My ultimate intention is actually to use the parcellation scheme proposed by Gordon et al. (<i>Cerebral Cortex</i>, Volume 26, Issue 1, 1 January 2016, Pages 288–303, <a href="https://doi.org/10.1093/cercor/bhu239">https://doi.org/10.1093/cercor/bhu239</a>)
though at this time I was using the atlas provided in the tutorial. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The problem I ran into is that I am trying to interpolate my brain’s mesh DOWN from 15002 to 8004 (to match the atlas), not up. As you pointed out, I have had some problems with other high resolution meshes, but in this case ft_sourceinterpolate
seemed to work — it just only worked for one of the two dimensions of my connectivity data. That is, it went from
<span style="color:black">a [15002×15002 double] to a [8004×15002 double]</span>. Of course it’s possible the interpolation for that first dimension was incorrect, but what confused me was that it did not interpolate the second dimension. (As I write this,
I’m wondering if I should simply try transposing the matrix and running the interpolation again!).
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I will try, as you suggest, downsampling the mesh externally and trying again. I’m not able to match the 8004 vertices perfectly, but perhaps if I drop it slightly below this number it will be able to interpolate up correctly.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Any other thoughts or suggestions are greatly appreciated as well.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal">Josh<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black"><fieldtrip-bounces@science.ru.nl> on behalf of "Seymour, Robert (Research Student)" <seymourr@aston.ac.uk><br>
<b>Reply-To: </b>FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Date: </b>Wednesday, April 25, 2018 at 5:48 PM<br>
<b>To: </b>"fieldtrip@science.ru.nl" <fieldtrip@science.ru.nl><br>
<b>Subject: </b>Re: [FieldTrip] ft_sourceinterpolate question<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><a name="_MailOriginalBody">Hi Josh, <o:p></o:p></a></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">It seems like you are using the HCP Glasser atlas ('A multi-modal parcellation of human cerebral cortex')? The atlas presented as part of the network analysis tutorial is designed for a cortical
mesh with 8004 vertices, rather than the 15002 you are using. I don’t believe ft_sourceinterpolate can currently cope with the surface-based transformation upwards from 8000—> 15000 vertices. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">To use the HCP atlas you will need to downsample the original 32k atlas in fs_LR space to 15000 space and transform to whichever standard-brain template you are using. This is non-trivial and
requires some functions from the HCP project (e.g. wb_command which can be found here: </span><a href="https://www.humanconnectome.org/software/workbench-command"><span style="mso-bookmark:_MailOriginalBody">https://www.humanconnectome.org/software/workbench-command</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody">).<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">If your mesh is created using Freesurfer you can use this script here:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"></span><a href="https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh"><span style="mso-bookmark:_MailOriginalBody">https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">If the mesh is not constructed using Freesurfer it will be tricker & I would recommend contacting the HCP mailing list.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Good luck!<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">Robert Seymour (Aston Brain Centre & Department of Cognitive Science, Macquarie University).<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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