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Thank you, I'm glad it was helpful! Feel free to email me (ebryson@ufl.edu) I'll definitely help if I can. You can also check out the 3D Slicer forum: discourse.slicer.org/ They've answered a lot of questions on there and it's a great place to start with troubleshooting an issue. Best, Rose

Hi, to clarify, do you want to calculate the volume of the object in the cropped scan? If so you'd use Segment Editor to assign that material to a new Segment and then use Segment Statistics to get the volume of that object. Or are you looking for the size of the cropped volume itself? - Rose

Hello! I use the "closed curve" tool in Markups to capture circumference. But yes you can get the measurement in the same way described in this video. Good luck! - Rose

Hi Maria, did you restart your Slicer application after installing? Go into the Extensions Manager and make sure that it did download (in the Installed Extensions tab at the top). If it is there, go to the main Slicer workspace (like the data module...) and click the magnifying glass icon by the drop down menu. Type in your extension and see if it pops up. Let m know if that did/didn't work. Good luck! -Rose

Thank you so much! I'm really glad it was helpful. - Rose

Hi, I can try to help. Could you briefly describe each step of what you did and I'll see if something was missed? This tutorial is specifically for .tif files, so I wanted to make sure that's the file-type you're trying to upload? Best, Rose

@@deleonlab I had uploaded an image in .IMA format. My steps are exactly the same as you. Do you think this is the reason? If that's the case, can I convert the document from .tif format to .IMA?

@@elifsu7033 This method is only for .tif files so you'd have to use another way for a .ima file. I haven't worked with them before but you could try just loading through the "Data" button in the top left corner, or converting it to a DICOM or .tif format. -Rose

Hi, In my experience as long as you have the 3D viewer on for all the segments you want to calculate statistics for, they'll all show up at once in the table. Try going to Segment Editor and make sure your liver and tumor segmentations are all visible and "Show 3D" is turned on. Now when you recalculate they should each show up as a line in the table. Let me know if this doesn't work and I can try to trouble shoot with you. Good luck! -Rose

Hi, can you explain a little more about what you're trying to do? Because it sounds like you could do that with this video tutorial, merging multiple models together into one object. Let me know and I'll see if I can help! -Rose

This happens to me sometimes when the coordinates for the model are far from the origin (0,0,0). Mirroring happens by multiplying one of the coordinates by -1. So, if your model has X coordinates in the 100-200 range, then the mirrored object may be there, but located in the -200 to -100 range. One quick check is to zoom way out and see if it appears. Another way to check this mathematically is to look at the coordinates for the model. If the values are consistently far from zero in one direction, you can use the Transform module to translate the model closer to the origin (or whatever location you want it to be). Let us know if this doesn't solve your problem! --Valerie

@@deleonlab Before mirroring my model is right at the centre of that globe, so it shouldn't have this problem? May I ask how to check the coordinates?

@@deleonlab Oh wait when I zoom away it does appear!

We have never successfully exported composite models from Meshlab. In our 3dPDF workflow, we export individual components (STL or OBJ format), use a third party software (e.g., Tetra 3dReviewer) to combine them into a U3D file, and then import to Acrobat to add javascript code and interface. I think there has to be a better (and free) way to build the U3D file and would love to hear any suggestions!! --Valerie

Once you've taken your angle/line, go to the "Markups" module, expand the "Measurements" dropdown menu on the left-hand side, select the measurements you want to see (length, angle, etc.) and the numerical value should appear. Let me know if this doesn't work and I can help you troubleshoot. -Rose

Yes, I believe you can. Go to the "Models" module, make sure your new 3D model is selected in the Node menu, click on the "Information" drop-down menu and your stats will be there. Let me know if that works for you!

Hi Daryl, You can erase at least two different ways. If you want something like the lasso you can erase using the "Scissor" tool (set to "Erase Inside" or "Erase Outside", in 2D or 3D space), I use that one on every segmentation project I do, it's very helpful. But if you have to be more precise I would use the Erase tool and paint the area you want taken out. Good luck!

@@deleonlab but when using scissor, it will also erase the backface right? it will erase all along in his path, so there is no lasso like eraser? by the way thanks for the reply, and thanks for your tutorials, i learnt many things.. im a newbie in 3D slicer, because it needs to my work .. im using new version 5.2 i think, i hope slicer will update lasso like eraser, coz it will helps u work faster or erase faster ...

@@daryldalore3625 Thank you, I'm really glad the tutorials were useful! You're correct, that scissor tool will erase everything in its path. Maybe try the eraser tool and select "Edit in 3D View" and "Sphere Brush." You might have more control that way. The Slicer team might have a better suggestions, check out their forum here: discourse.slicer.org/. They respond pretty quickly to questions and have a great community of users that could give suggestions.

Agreed! Thanks for commenting!!

Hi, I haven't used those programs so I'm not sure. You might have to check with their customer support to find the best file format to import coordinates. Good luck! - Rose

I would segment and save each ROI separately, saving them as 3D models, and then merge the models into one file. That way you can color them distinctively but have them all be in anatomical position. Here's a tutorial I made on merging multiple models in Slicer: ruclips.net/video/mhCS5gsR410/видео.html -Rose

Thank you so much for your answer; I will try this method and let you know about the outcome. Thank you again.

Hi Mohammed, Thank you, I'm glad you found it helpful! There are a few ways to make endocasts in 3D Slicer, the method I use for my research is Wrap Solidify, I made a tutorial of it here: ruclips.net/video/H1U07_UW9lI/видео.html Good luck! -Rose

Hi Mohammed, I'm happy to try and help, my email is ebryson@ufl.edu. I'd also suggest posting your question to the 3D Slicer forum: discourse.slicer.org/c/support/11. They usually respond very quickly and know a lot more than I do! Talk soon, Rose

Can you confirm that you resampled the volume to a reference volume in another location/orientation? Even if the volume kept the same ijk coordinates (0 to i, 0 to j, 0 to k), each voxel should correspond to a different position in the world coordinates. I don't use ijk coordinates for my work, but I thought they always start with an origin of (0,0,0). If you transform the volume, you'd need to use anatomical or world coordinates to capture the spatial transformation.

​@@deleonlab Thanks for the response! It worked! In the very beginning, I didn't use a reference volume because I was using the "resample scalar volume", which doesn't have that option. Later on, when I switched to the one you used "scalar/vector/DWI", for reference volume, I just selected the same one (as the input volume), and it didn't work. I didn't pay attention to it because I thought it was just about spacing, voxel size etc, nothing related to the IJK system. Now I just tried it again using the initial (before linear transform) volume as the reference volume and it worked! The changes are done in the IJK system! Also want to thank you for commenting on the resampling without hardening the transform, which does make a difference! I think I still need to spend more time figuring out how these concepts work together, but at least I got what I need in the short term! You are a life-saver! Thanks a ton!!

Just to make an addition here, in case someone else might benefit from it - during the resampling, make sure the correct linear transform is selected as well!

@@KitkatTrading2024 I'm so glad this was helpful for you! - Valerie

I was doing the exact same thing! So much easier just to do everything in the same place. Glad it helped! - Rose

@deleonlab That was soooo useful! I was using Meshlab as well!!

I'm so glad they were helpful!

Hi Jon, It could be losing it's texture information because of the format you're saving it in, how did you save it (.stl, .ply, .obj?) If you haven't saved it yet and the color was lost right after you merged the models, I haven't had that happen before. If so, try it again and let me know if you have the same result. Good luck! -Rose