
<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><p class=""><span style="font-style: inherit; text-decoration-line: none;" class="">Hello,</span></p><p class=""><span style="font-style: inherit; text-decoration-line: none;" class="">I’ve been editing my segmentation results with Freeview following the instructions on this page: <a href="https://simnibs.github.io/simnibs/build/html/documentation/command_line/headreco.html" class="">https://simnibs.github.io/simnibs/build/html/documentation/command_line/headreco.html</a> My aim is to correct the CSF since it overflows to bone in some of the segmentations. After I edit the segmentation on the binary mask in the /mask_prep folder (in this case MASK_CSF.nii.gz), I run headreco surfacemesh and headreco volumemesh, the colors of the segmentation changes, these are saved in </span><span style="text-decoration-line: none; font-style: inherit;" class="">, SubID_</span><span style="text-decoration-line: none; font-style: inherit;" class="">final_contr.nii file</span><span style="text-decoration-line: none; font-style: inherit;" class="">. </span><span style="text-decoration-line: none; font-style: inherit;" class="">H</span><span style="font-style: inherit; text-decoration-line: none;" class="">owever, the lines saved in head_contr.fmesh and brain_contr.fmesh</span><font style="font-style: inherit;" class=""><font color="black" class=""><span dir="ltr" id="x_divtagdefaultwrapper" style="font-style: inherit;" class=""> </span></font></font><span style="font-style: inherit; text-decoration-line: none;" class="">that define the boundary between bone and CSF are not changing.</span></p><p class=""><span style="font-style: inherit; text-decoration-line: none;" class="">I tried to do these steps with CAT12 as well as without CAT12, with - -no -cat command. However, both of them resulted in the same way. Am I successfully </span><span style="font-style: inherit; text-decoration-line: none;" class="">editing the segmentation so that the magnetic field simulation done by SimNIBS will use the correct tissue borders?</span><span style="font-style: inherit; text-decoration-line: none;" class=""> Or, do I have to apply something else in order to edit the line boundaries as well?</span></p><div class="">Thank you for your help and answers in advance.</div><div class="">Best wishes,</div><div class="">Gülce</div><div class=""><br class=""></div><div class="">

<meta charset="UTF-8" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div><font color="#606060" class="">Gülce Lale</font></div><div><font color="#606060" class="">MSc Neurosciences</font></div></div>

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