<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body>
<div class="" style="word-wrap:break-word">Dear Jeff,
<div class=""><br class="">
</div>
<div class="">Let me forward your question to the discussion list.</div>
<div class=""><br class="">
</div>
<div class="">Dear list,</div>
<div class=""><br class="">
</div>
<div class="">Jeff is encountering some coregistration problems, which may be FieldTrip related, but also could be a user error. Perhaps somebody has encountered them before. Let us know if you have a solution.</div>
<div class=""><br class="">
</div>
<div class="">The 45 degrees tilt looks odd. If this image was produced after reslicing the to-MNI-coregistered-image something went wrong with the realignment. If this image was produced prior to the reslicing, something funky has gone wrong with the acquisition
sequence.</div>
<div class=""><br class="">
</div>
<div class="">I don’t know anything about the specifics of Brainstorm, so I am afraid I cannot help there.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class=""><br class="">
</div>
<div class="">Jan-Mathijs</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">
<div class="" style="word-wrap:break-word">
<div class="" style="word-wrap:break-word">
<div class="" style="word-wrap:break-word">J.M.Schoffelen, MD PhD<br class="">
Senior Researcher, VIDI-fellow - PI, language in interaction<br class="">
Telephone: +31-24-3614793</div>
<div class="" style="word-wrap:break-word">Physical location: room 00.028</div>
<div class="" style="word-wrap:break-word">Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands<br class="">
<br class="">
<br class="">
</div>
</div>
</div>
</div>
</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">Begin forwarded message:</div>
<br class="x_Apple-interchange-newline">
<div class="" style="margin-top:0px; margin-right:0px; margin-bottom:0px; margin-left:0px">
<span class="" style=""><b class="">From: </b></span><span class="" style="">K Jeffrey Eriksen <<a href="mailto:eriksenj@ohsu.edu" class="">eriksenj@ohsu.edu</a>><br class="">
</span></div>
<div class="" style="margin-top:0px; margin-right:0px; margin-bottom:0px; margin-left:0px">
<span class="" style=""><b class="">Subject: </b></span><span class="" style=""><b class="">RE: [HCP-Users] hcp_anatomy.m needs an hsfile?</b><br class="">
</span></div>
<div class="" style="margin-top:0px; margin-right:0px; margin-bottom:0px; margin-left:0px">
<span class="" style=""><b class="">Date: </b></span><span class="" style="">11 March 2017 at 02:47:33 GMT+1<br class="">
</span></div>
<div class="" style="margin-top:0px; margin-right:0px; margin-bottom:0px; margin-left:0px">
<span class="" style=""><b class="">To: </b></span><span class="" style="">"Schoffelen, J.M. (Jan Mathijs)" <<a href="mailto:jan.schoffelen@donders.ru.nl" class="">jan.schoffelen@donders.ru.nl</a>><br class="">
</span></div>
<br class="">
<div class="">
<div class="x_WordSection1" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">Hello again,</span></div>
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">I encountered a problem when I tried to import into Brainstorm, even though I thought I had the transform text file correct. After importing the anatomy in Brainstorm,
it was displayed with the brain rotated by 45 degrees in all axes. I then realized the I had visualized the registration of the headshape to the scalp surface and that looked good, but I had never visualized the MNI registration.</span></div>
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">I went back into the HCP scripts and found where the MNI registration could be visualized and discovered the 45 degree rotation seemed to occur there. So I thought maybe
our local HCP pipeline did something unusual. To test this I ran these three conditions:</span></div>
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
<div class="" style="margin:0in 0in 0.0001pt 0.5in; font-size:12pt; font-family:'Times New Roman',serif; text-indent:-0.25in">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"><span class="">1.<span class="" style="font-style:normal; font-variant:normal; font-weight:normal; font-size:7pt; line-height:normal; font-family:'Times New Roman'"> <span class="x_Apple-converted-space"> </span></span></span></span><span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">My
hcp_anatomy_egi.m with our local HCP-pipeline produced T1</span></div>
<div class="" style="margin:0in 0in 0.0001pt 0.5in; font-size:12pt; font-family:'Times New Roman',serif; text-indent:-0.25in">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"><span class="">2.<span class="" style="font-style:normal; font-variant:normal; font-weight:normal; font-size:7pt; line-height:normal; font-family:'Times New Roman'"> <span class="x_Apple-converted-space"> </span></span></span></span><span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">original
hcp_anatomy.m with our local T1</span></div>
<div class="" style="margin:0in 0in 0.0001pt 0.5in; font-size:12pt; font-family:'Times New Roman',serif; text-indent:-0.25in">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"><span class="">3.<span class="" style="font-style:normal; font-variant:normal; font-weight:normal; font-size:7pt; line-height:normal; font-family:'Times New Roman'"> <span class="x_Apple-converted-space"> </span></span></span></span><span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">original
hcp_anatomy.m with downloaded HCM_MEG_pipeline produced T1</span></div>
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">All three had the same apparent problem, shown on the attached images. I am quite puzzled by this since they are all the same, yet Brainstorm only imports #3 correctly
(not counting #2 which is mixed).</span></div>
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">I put all three cases in the attached Word doc, with the Brainstorm registration display and the HCP headshape registration display.</span></div>
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">-Jeff</span></div>
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
<div class="">
<div class="" style="border-style:solid none none; border-top-color:rgb(181,196,223); border-top-width:1pt; padding:3pt 0in 0in">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<b class=""><span class="" style="font-size:10pt; font-family:Tahoma,sans-serif">From:</span></b><span class="" style="font-size:10pt; font-family:Tahoma,sans-serif"><span class="x_Apple-converted-space"> </span>Schoffelen, J.M. (Jan Mathijs) [<a href="mailto:jan.schoffelen@donders.ru.nl" class="">mailto:jan.schoffelen@donders.ru.nl</a>]<span class="x_Apple-converted-space"> </span><br class="">
<b class="">Sent:</b><span class="x_Apple-converted-space"> </span>Wednesday, March 08, 2017 8:52 AM<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span>K Jeffrey Eriksen<br class="">
<b class="">Subject:</b><span class="x_Apple-converted-space"> </span>Re: [HCP-Users] hcp_anatomy.m needs an hsfile?</span></div>
</div>
</div>
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
</div>
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
Hi Jeff,<span class="x_Apple-converted-space"> </span></div>
<div class="">
<div class="">
<blockquote class="" style="margin-top:5pt; margin-bottom:5pt">
<div class="">
<p class="x_MsoNormal" style="margin:12pt 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">I made it all the way through hcp_anatomy_EGI.m (my version substituting ‘egi’ for ‘bti’. Amazing!</span></p>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
</div>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">I could not figure out how to do the interactive fine registration of the EGI electrode “headshape” to the scalp surface – where is that documented?</span></div>
</div>
</div>
</blockquote>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
</div>
</div>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
Well it’s not extensively documented, but in the crude GUI you can fiddle around with translation and rotation parameters to move the electrode point cloud closer to the headsurface mesh, created from the MRI segmentation.</div>
</div>
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<br class="">
<br class="">
</div>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">The main remaining problem is that the BTI coordinate system has the X-axis toward the nasion, and the Y-axis toward the LPA. The EGI coordinate system has the X-axis
toward the RPA and the Y-axis toward the nasion. Can you suggest the best way to change hcp_anatomy_EGI.m to reflect this?</span></div>
</div>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
</div>
</div>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
Well, it sounds as if the EGI has an RAS convention, which may be similar to the ‘neuromag’ convention (as per <a href="http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined" class="" style="color:purple; text-decoration:underline">http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined</a>)</div>
</div>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
</div>
</div>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
It could be that changing the required coordinate system (coordsys) to ‘neuromag’ while specifying the fiducials in ft_volumerealign (rather than ‘bti’) would do the trick.</div>
</div>
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<br class="">
<br class="">
</div>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">Each of the supported coordinates systems must have some kind of master definition somewhere in the code, and that would be the best place to define the EGI system.
I think it is similar to the BESA system.</span></div>
</div>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
</div>
</div>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
The code that has the ‘intelligence’ to map the specification of defined fiducial/landmark locations is in<span class="x_Apple-converted-space"> </span><a href="https://github.com/fieldtrip/fieldtrip/blob/master/utilities/ft_headcoordinates.m" class="" style="color:purple; text-decoration:underline">https://github.com/fieldtrip/fieldtrip/blob/master/utilities/ft_headcoordinates.m</a></div>
</div>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
with a typo in line48/49 I noticed just now.</div>
</div>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
</div>
</div>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
Feel free to suggest a new coordinate system if needed. Perhaps this is best done through the fieldtrip discussion list.</div>
</div>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
</div>
</div>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
Best,</div>
</div>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
Jan-Mathijs</div>
</div>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
</div>
</div>
<div class="">
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
</div>
</div>
<div class="" style="margin:0in 0in 0.0001pt; font-size:12pt; font-family:'Times New Roman',serif">
<br class="">
<span class="" style="font-size:12pt"> </span></div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
</div>
</div>
<div class="" style="word-wrap:break-word">
<div class="">
<div>
<blockquote type="cite" class="">
<div class=""></div>
</blockquote>
</div>
<br class="">
</div>
<br class="">
<br class="">
</div>
</body>
</html>