<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Aptos;}
@font-face
{font-family:"Helvetica Neue";
panose-1:0 0 0 0 0 0 0 0 0 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
font-size:12.0pt;
font-family:"Aptos",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
span.EmailStyle20
{mso-style-type:personal-compose;
font-family:"Aptos",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:11.0pt;
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 90.0pt 72.0pt 90.0pt;}
div.WordSection1
{page:WordSection1;}
/* List Definitions */
@list l0
{mso-list-id:1106776707;
mso-list-template-ids:-517977360;}
@list l0:level1
{mso-level-tab-stop:36.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level2
{mso-level-tab-stop:72.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level3
{mso-level-tab-stop:108.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level4
{mso-level-tab-stop:144.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level5
{mso-level-tab-stop:180.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level6
{mso-level-tab-stop:216.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level7
{mso-level-tab-stop:252.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level8
{mso-level-tab-stop:288.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level9
{mso-level-tab-stop:324.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
ol
{margin-bottom:0cm;}
ul
{margin-bottom:0cm;}
--></style>
</head>
<body lang="EN-GB" link="blue" vlink="purple" style="word-wrap:break-word">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">Hi,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">I think it's best not to change your headshape fiducials. These fiducials define the coordinate system relative to which the points in headshape.pos
are specified. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">The problem with the fiducials not being well-defined after headshape refinement could be due to two reasons:<o:p></o:p></span></p>
<ol style="margin-top:0cm" start="1" type="1">
<li class="MsoNormal" style="mso-list:l0 level1 lfo1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">As Jan-Mathijs nicely pointed out, your headshape might not have enough points, causing the ICP to worsen your coregistration.<o:p></o:p></span></li><li class="MsoNormal" style="mso-list:l0 level1 lfo1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">The fiducials from the headshape might be incorrect, as you believe.<o:p></o:p></span></li></ol>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">Given these issues, I wouldn't trust the headshape. I suggest performing only step 1 and skipping the headshape refinement.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">Best,
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">Konstantinos<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;font-family:"Calibri",sans-serif;mso-fareast-language:EN-US">PS. Theoretically, you could change your headshape fiducials to match your fiducials from step 1 and then adjust headshape.pos relative to the new
coordinate system. However, can you fully trust the <i>manually</i> selected points in step 1? My advice is to ensure in the future that your headshape fiducials are well-specified during the experimental acquisition (e.g., by using pen markings or earmolds).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;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>Parker via fieldtrip<br>
<b>Sent:</b> Friday, July 26, 2024 2:34 PM<br>
<b>To:</b> fieldtrip@science.ru.nl<br>
<b>Cc:</b> Parker <pjosephsmith6791@gmail.com><br>
<b>Subject:</b> Re: [FieldTrip] Ft_VolumeRealign Shifting Manually Set Fiducials<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">I appreciate your feedback. Given that my manually selected fiducials don't agree with the ones stored in the MEG headshape variable (which were set up before by the researcher prior to running the scan), is it acceptable to first modify
the headshape variable by removing the fiducial field prior to inputting it into the ft_voluemrealign function to use ICP. <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">(I understand ICP would benefit from more headshape points but I notice it still works well and that ICP does not seem like the source of the issue here but rather just the disagreeing fiducials.)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Thank you again!<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">On Mon, Jul 8, 2024 at 9:22<span style="font-family:"Arial",sans-serif"> </span>PM Parker <<a href="mailto:pjosephsmith6791@gmail.com">pjosephsmith6791@gmail.com</a>> wrote:<o:p></o:p></p>
</div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm">
<div>
<p style="margin:0cm;min-height:25px"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">Hi,</span><span style="font-size:15.0pt;font-family:"Helvetica Neue",serif"><o:p></o:p></span></p>
<p style="margin:0cm;min-height:15px"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"><o:p> </o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">I have a question about MEG anatomical coregistration, particularly when using ft_volumerealign to do fiducial selection and coregistration refinement with headshape and
ICP.<o:p></o:p></span></p>
<p style="margin:0cm;min-height:15px"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"><o:p> </o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">My current steps with ft_volumerealign are: 1) adding ‘coordsys = neuromag’ field to my mri by manually selecting N,LPA,RPA fiducials 2) refining fit with cfg.method = 'headshape'
and cfg.headshape.icp = 'yes' with the headshape provided from my MEG file 3) plotting realigned mri to do a visual check on coordinate system with ft_determine_coordsys. (My code is also below)<o:p></o:p></span></p>
<p style="margin:0cm;min-height:15px"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"><o:p> </o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">After doing the refinement step, I notice the fiducial positions I initially set are almost always shifted. I have linked a picture for example showing 1) coordinates after
my fiducial selection, 2) coordinates after headshape refinement - <a href="https://drive.google.com/drive/folders/13SAOL7FYM2yCiUPTV9StJh1HfNr_hDGP?usp=sharing" target="_blank">https://drive.google.com/drive/folders/13SAOL7FYM2yCiUPTV9StJh1HfNr_hDGP?usp=sharing</a><o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"><o:p> </o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">In the second image, the nasion is shifted upwards to what I would consider an incorrect position. (I also noticed that when plotting my source model, the source points
appear to be slightly shifted up compared to one of the subjects from FT tutorials). <o:p></o:p></span></p>
<p style="margin:0cm;min-height:15px"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"><o:p> </o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">I am guessing the reason why, for ex, my nasion fiducial shift upwards after headshape refinement is because my headshape variable from my MEG file has a fiducial field,
which are instead the fiducials that are being used instead of my manually selected ones. <o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"><o:p> </o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">Nevertheless, I was wondering how I could still perform headshape refinement with ICP and ensure MRI/MEG shape alignment but instead re select the fiducial positions. <o:p></o:p></span></p>
<p style="margin:0cm;min-height:15px"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"><o:p> </o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">I appreciate the help,<o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">Parker<o:p></o:p></span></p>
<p style="margin:0cm;min-height:15px"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"><o:p> </o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">Step 1 - Fiducial selection<o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg = [];<o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg.method = 'interactive';<o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg.coordsys = 'neuromag'; <o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg.flip = 'no';<o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">mri_realigned = ft_volumerealign(cfg, mri);<o:p></o:p></span></p>
<p style="margin:0cm;min-height:15px"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"><o:p> </o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">Step 2 - headshape refinement<o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg = [];<o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg.method = 'headshape';<o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg.headshape.headshape = My_MEG_fif_file;<o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg.headshape.icp = 'yes';<o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">mri_realigned = ft_volumerealign(cfg,mri_realigned);<o:p></o:p></span></p>
<p style="margin:0cm;min-height:15px"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"><o:p> </o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">Step 3 - Plotting Realigned mri + coordinate system:<o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg = [];<o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">cfg.method = 'headshape';<o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">shape = ft_read_headshape(filename);<o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">shape = ft_convert_units(shape,'mm');<o:p></o:p></span></p>
<p style="margin:0cm;min-height:15px"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif"> <o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">ft_determine_coordsys(mri_realigned, 'interactive', 'no');<o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">hold on; <o:p></o:p></span></p>
<p style="margin:0cm"><span style="font-size:10.0pt;font-family:"Helvetica Neue",serif">drawnow; <o:p></o:p></span></p>
<p 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">ft_plot_headshape(shape);<o:p></o:p></span></p>
</div>
</blockquote>
</div>
</div>
</body>
</html>