<div dir="ltr">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. <div><br></div><div>(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.)<br></div><div><br></div><div>Thank you again!</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Jul 8, 2024 at 9:22 PM Parker <<a href="mailto:pjosephsmith6791@gmail.com">pjosephsmith6791@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">
<p style="margin:0px;font:20px "Helvetica Neue";min-height:25px"><span style="font-size:13px">Hi,</span><b></b></p><p style="margin:0px;font:13px "Helvetica Neue";min-height:15px"><br></p><p style="margin:0px;font:13px "Helvetica Neue"">I have a question about MEG anatomical coregistration, particularly when using ft_volumerealign to do fiducial selection and coregistration refinement with headshape and ICP.</p><p style="margin:0px;font:13px "Helvetica Neue";min-height:15px"><br></p><p style="margin:0px;font:13px "Helvetica Neue"">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)</p><p style="margin:0px;font:13px "Helvetica Neue";min-height:15px"><br></p><p style="margin:0px;font:13px "Helvetica Neue"">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></p><p style="margin:0px;font:13px "Helvetica Neue""><br></p><p style="margin:0px;font:13px "Helvetica Neue"">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).<span> </span><br></p><p style="margin:0px;font:13px "Helvetica Neue";min-height:15px"><br></p><p style="margin:0px;font:13px "Helvetica Neue"">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. </p><p style="margin:0px;font:13px "Helvetica Neue""><br></p><p style="margin:0px;font:13px "Helvetica Neue"">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.<span> </span></p><p style="margin:0px;font:13px "Helvetica Neue";min-height:15px"><br></p><p style="margin:0px;font:13px "Helvetica Neue"">I appreciate the help,</p><p style="margin:0px;font:13px "Helvetica Neue"">Parker</p><p style="margin:0px;font:13px "Helvetica Neue";min-height:15px"><br></p><p style="margin:0px;font:13px "Helvetica Neue"">Step 1 - Fiducial selection</p><p style="margin:0px;font:13px "Helvetica Neue"">cfg = [];</p><p style="margin:0px;font:13px "Helvetica Neue"">cfg.method = 'interactive';</p><p style="margin:0px;font:13px "Helvetica Neue"">cfg.coordsys = 'neuromag';<span> </span></p><p style="margin:0px;font:13px "Helvetica Neue"">cfg.flip <span style="white-space:pre-wrap"> </span><span style="white-space:pre-wrap"> </span>= 'no';</p><p style="margin:0px;font:13px "Helvetica Neue"">mri_realigned = ft_volumerealign(cfg, mri);</p><p style="margin:0px;font:13px "Helvetica Neue";min-height:15px"><br></p><p style="margin:0px;font:13px "Helvetica Neue"">Step 2 - headshape refinement</p><p style="margin:0px;font:13px "Helvetica Neue"">cfg = [];</p><p style="margin:0px;font:13px "Helvetica Neue"">cfg.method = 'headshape';</p><p style="margin:0px;font:13px "Helvetica Neue"">cfg.headshape.headshape = My_MEG_fif_file;</p><p style="margin:0px;font:13px "Helvetica Neue"">cfg.headshape.icp = 'yes';</p><p style="margin:0px;font:13px "Helvetica Neue"">mri_realigned = ft_volumerealign(cfg,mri_realigned);</p><p style="margin:0px;font:13px "Helvetica Neue";min-height:15px"><br></p><p style="margin:0px;font:13px "Helvetica Neue"">Step 3 - Plotting Realigned mri + coordinate system:</p><p style="margin:0px;font:13px "Helvetica Neue"">cfg = [];</p><p style="margin:0px;font:13px "Helvetica Neue"">cfg.method<span> </span>= 'headshape';</p><p style="margin:0px;font:13px "Helvetica Neue"">shape <span> </span>= ft_read_headshape(filename);</p><p style="margin:0px;font:13px "Helvetica Neue"">shape = ft_convert_units(shape,'mm');</p><p style="margin:0px;font:13px "Helvetica Neue";min-height:15px"><span> </span></p><p style="margin:0px;font:13px "Helvetica Neue"">ft_determine_coordsys(mri_realigned, 'interactive', 'no');</p><p style="margin:0px;font:13px "Helvetica Neue"">hold on;<span> </span></p><p style="margin:0px;font:13px "Helvetica Neue"">drawnow;<span> </span></p><p style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:13px;line-height:normal;font-family:"Helvetica Neue"">
</p><p style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-variant-alternates:normal;font-kerning:auto;font-feature-settings:normal;font-stretch:normal;font-size:13px;line-height:normal;font-family:"Helvetica Neue"">ft_plot_headshape(shape);</p></div>
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