<meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr"><div dir="ltr"><div dir="ltr">Hi Luca,<div><br></div><div>Let me CC the mailing list on this email given that others might be running into similar issues now or in the future. The short answer is that based on this information I can only guess as to why the electrodes are outside the brain (issue #1), and why they appear in the other hemisphere (issue #2). </div><div><br></div><div>Regarding #1, can you confirm that the apparent mislocalization only pertains to the surface mesh and not the MR volume? You can verify this by reading in the freesurfer-polished MRI (/freesurfer/mri/T1.mgz) and visualize this scan along with the previously localized electrodes using <i>ft_electrodeplacement</i>. For a background, FreeSurfer uses different coordinate systems for volumetric images and for surface meshes extracted from those images. The call to <i>mri_convert</i> at<a href="http://www.fieldtriptoolbox.org/tutorial/human_ecog/"> step 6 </a>works around this default feature by forcing the two to have the same coordinate system, meaning you won't need to convert electrode locations when plotting them with either modality. It's possible something did not well during this step for you, though that would not explain the left-right flip.</div><div><br></div><div>As for #2, it seems likely indeed there's a left-right flip in the CT scan. You might want to thoroughly check whether you correctly identified the left-right axis, i.e. it could be any of the x, y, or z-axes depending on the native coordinate system in which the scan came. And then, as you said, check whether that axis runs from left to right or right to left, as demonstrated in the <a href="https://static-content.springer.com/esm/art%3A10.1038%2Fs41596-018-0009-6/MediaObjects/41596_2018_9_MOESM6_ESM.mp4">movie</a> corresponding to step 3 (and Box 3 of the original <a href="https://www.nature.com/articles/s41596-018-0009-6">protocol</a>). Fusion step 14 produces a plot of the CT and MR overlaid, providing a final checkpoint of your preprocessing. That is, the CT and MR need to show a snug fit here. A left-right flip, by the way, could affect the precision of the final electrode locations given that the fusion step would not produce an optimal match between CT and MR unless the participant's brain/head were perfectly symmetrical.</div><div><br></div><div>As a side note, make sure to specify the <i>cfg.spmmethod = 'new'</i> option when calling <i>ft_volumenormalize</i>, as in the online tutorial (step 26). Our experience is that the new algorithm works better than the previous one for projecting electrodes to MNI space.</div><div><br></div><div>Best,</div><div>Arjen</div><div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Jul 4, 2019 at 9:13 AM Luca Iemi <<a href="mailto:luca.iemi@gmail.com">luca.iemi@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi Arjen, <div>I hope my email finds you well.</div><div>I finished the anatomical workflow for the first patient (see attached). This is the first time that I completed the whole pipeline and I have some very basic questions (I read the article as well as the online tutorial but couldn't find the answers). No one in my group has any experience with this so I am asking you. I apologize if my questions sound very basic.</div><div><br></div><div>1) I plotted the cortical hulls for left and right hemispheres and overlayed the depth electrodes as localized in <span style="font-family:Courier;font-size:10px"><font color="#000000">ft_electrodeplacement </font></span>(red) and the same electrodes transformed in MNI space (black). </div><div>The problem is that some of these electrodes lie outside the cortical hulls. This problem didn't appear at the <span style="color:rgb(0,0,0);font-family:Courier;font-size:10px">ft_electrodeplacement</span> stage. I wonder if you could perhaps point me to the part of the anatomical workflow I may be doing incorrectly.</div><div><br></div><div>2) Also another quick question: both the CT and the MRI have a left-to-right orientation (the axis increases to the right according to <span style="font-family:Courier;font-size:10px">ft_determine_coordsys</span>). The implant was on the left hemisphere, but my reconstruction shows it on the right hemisphere. Should I flip the scans? How can I do that and at what stage should I become aware of this problem?</div>
<p class="gmail-m_411697550314353207gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:Courier;min-height:14px"><br></p><div>Thanks for your help<br></div><div>Best wishes, </div>
<div><br></div><div><div><br></div>-- <br><div dir="ltr" class="gmail-m_411697550314353207gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><span style="font-family:arial,helvetica,sans-serif;font-size:small"><font color="#999999"><br></font></span></div><div><span style="font-family:arial,helvetica,sans-serif;font-size:small"><font color="#999999">Luca</font></span></div><div><span style="font-family:arial,helvetica,sans-serif;font-size:small"><font color="#999999"><br></font></span></div><div><span style="font-family:arial,helvetica,sans-serif;font-size:small"><font color="#999999"><br></font></span></div><div><span style="font-family:arial,helvetica,sans-serif;font-size:small"><font color="#999999">--</font></span></div><div><span style="font-family:arial,helvetica,sans-serif;font-size:small"><font color="#999999">Dr. Luca Iemi</font></span></div><div><span style="font-family:arial,helvetica,sans-serif;font-size:small"><font color="#999999">Post-Doc, </font></span><span style="color:rgb(153,153,153);font-family:"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:12.88px;letter-spacing:normal">Department of Neurological Surgery, </span><span style="color:rgb(153,153,153);margin:0px;padding:0px;border:0px;outline:0px;vertical-align:baseline;font-stretch:inherit;font-size:12.88px;line-height:inherit;font-family:"Helvetica Neue",Helvetica,Arial,sans-serif;letter-spacing:normal">Columbia University College of Physicians and Surgeons</span><span style="color:rgb(153,153,153);font-family:"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:12.88px;letter-spacing:normal">, New York, NY 10032</span></div><div><font color="#999999"><br></font></div><div><font color="#999999"><br></font></div><div><font color="#999999"><span style="font-size:12.8px">This </span><span style="font-size:12.8px">email</span><span style="font-size:12.8px"> may contain material that is confidential and/or privileged for the </span><span style="font-size:12.8px">sole</span><span style="font-size:12.8px"> use of the </span><span style="font-size:12.8px">intended</span><span style="font-size:12.8px"> recipient. Any review, reliance or distribution by others or forwarding without express permission is strictly prohibited. If you are not the </span><span style="font-size:12.8px">intended</span></font><span style="font-size:12.8px"><font color="#999999"> recipient, please contact the sender and delete all copies.</font><br></span><font color="#666666" face="arial, helvetica, sans-serif" size="2"><br></font></div></div></div></div></div></div></div></div></div></div></div></div>
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