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<p>Hi <span>Ti Chun Hang Eden,</span></p>
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<p><span>I haven't tried the stroke tool, so not sure what it outputs, but if the stroke lesion is segmented out separately you could assign that to CSF in the mask_prep folder (after binarization).</span></p>
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<p><span>In the final mesh the lesioned area would then be CSF, but you can afterwards relabel it back to stroke lesion using the segmentation mask if you want.</span></p>
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<p><span>Best,<br>
Oula</span></p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Simnibs-discuss <simnibs-discuss-bounces@drcmr.dk> on behalf of TI, Chun Hang Eden <1155138422@link.cuhk.edu.hk><br>
<b>Sent:</b> Thursday, November 26, 2020 2:14:14 AM<br>
<b>To:</b> simnibs-discuss@drcmr.dk<br>
<b>Subject:</b> [Simnibs-discuss] About the usage of custom CAT12 segmentation</font>
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Dear Sir/Madam, </div>
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I have been using SIMNIBS headreco segmentation to generate cortical surface reconstruction for stroke patients, knowing CAT12 is not optimized for these types of brains. </div>
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The newest version of CAT12 includes a function (Stroke Lesion Correction), which produces a better segmentation result after my inspection. Is there a way to incorporate these segmentation results directly, to proceed to the next stage?</div>
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I tried to use the segmentation results from that, to replace the results in /segments/cat directories, and binarized the segmentation mask. However, when I run the preparecat function, I encounter the following errors. </div>
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<img size="203203" contenttype="image/png" unselectable="on" tabindex="-1" style="user-select: none; width: 766.931px; height: 346.526px;" data-imgsize="custom" width="766.9314720812182" height="346.52637614678895" data-outlook-trace="F:1|T:1" src="cid:df45b0e2-26fb-4b88-a9b2-6d60ad27ee85"></div>
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I suspect that the error results from the difference of the number of vertices of the mesh generated from the initial preparevol command and the custom segmentation results from new CAT12. </div>
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Is there any way to generate a .off file based on the new CAT12 features? </div>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">I have been using Simnibs for a long time and really appreciate your team's effort in maintaining and updating the software for better progression of this
research field. Look forward to your reply</span></div>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><br>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Best regards,</span></div>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"> </span></div>
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<div><font face="Calibri,Arial,Helvetica,sans-serif"><b>Ti Chun Hang Eden</b></font><u></u><br>
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<div style="color:rgb(0,0,0); font-size:12pt">PhD, Department of Biomedical Engineering</div>
<div style="color:rgb(0,0,0); font-size:12pt">The Chinese University of Hong Kong</div>
<div style="color:rgb(0,0,0); font-size:12pt">Email: 1155138422@link.cuhk.edu.hk</div>
<div style="color:rgb(0,0,0); font-size:12pt">Mobile: +852 91339153</div>
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