I've spent dozens of hours in Avizo 9 segmenting a lizards skull. I have 40 different "materials" corresponding to different bones. The project is pretty big.
I want to make a reconstruction of the missing parts of the skull in Maya (maybe you could recommend smth better or simpler than Maya for mac?).
So, I need to export the entire project to Maya without loosing labels, ie I need to edit different bones separately.
Hi, if you want to edit each bone separately, then I would recommend generating a surface file for each label individually, and export it as a Wavefron *.obj file (you do that by right clicking on the green module representing your surface (.surf) and then selecting the button with the folder&arrow pointing to the right (see first screenshot attached below).
However, that will likely result in a very large file, and I would recommend resizing each surface before exporting (or Maya will likely crash). This is done by decreasing the number of faces of your 3D surface. If you click on the green surface module (.surf) and select the button with the inverted red triangle (see second screenshot below) you will be able to decrease the number of faces to a more reasonable number (1,000,000 is usually good enough). After writing the number of faces you want click "simplify now". At this point you can export a much more manageable .obj file.
Alessandro, thank you very much for your complete answer!
Could you tell me how to generate surface separately for chosen material? The thing is when I generating surface Avizo creating the whole 3d model and I don't see the option to choose required material...I've tried many ways but still did not achieve success.
Also, I think that it will be a challenge to put all the bones separately in Maya in right position unless .obj remembers the relative position in space...
And by the way, how did you learn this things about Avizo? RTFManual? Special courses?
Hi, in an older version of Avizo it was necessary to create a label field with only that (or those) label(s) which I wanted to export. I found no option to export only specific labels from one labelfield. But you can create several labelfields within one Avizo-project...
I agree with the above. I segment bones into a separate label field if I want them separated form other bones. Then you can generate a surface model for each of the label fields, and be able to export them separately. Amira/Avizo has you use different materials, but that gets glitchy when you have a lot, and does not allow you to manipulate them separately.
Hi, Achim!
No way! I don't think that there is no possibility to export specific labels. In that case what is a point to give ability of creating lots of labels?
if so, it's sad...
Hello again, I think you may find the link below useful, especially the part about the Arithmetic module. That's how you can separate individual labels and render and export each separately. With regard to your other question, I have learned these things a bit reading the manual, a bit talking to people, and a bit looking for tutorials online.
http://avsl.cct.lsu.edu/vizclass_illustration.html
Although my (quite basic) question is not related to your query, does anybody know how to put a scale on snapshot of CT scan (I want to extract jpeg file with the scale in millimeters). THANX!
Hi Sonja,
you can easily add a scalebar to the viewer window in Avizo if the dataset you imported has the correct voxel size. If that is the case, then you only have to follow these steps (see also attached image):
1 - Make sure you remove parallax distortion by selecting "orthogonal view". If you don't your measurements will be wrong.
2 - Select the "2D length" measurement tool.
3 - Place your scalebar as a measurement on the screen (just click on start and end points). You can drag and adjust these points around if necessary.
The number next to the scale bar represents how many units it's long. In the example I provided it's 5000 units long because my units are in microns. The units on the screen are dictated by whatever units you used to input the voxel size when you loaded the dataset into Avizo. In your case you can either input the voxel size in mm, or just do a simple conversion. It's important to remember that if you zoom in/out on your specimen the scalebar will not update (only 3D measurement do, but those need to be placed on your specimen), and you will have to place a new scalebar.
4 - You can adjust the thickness of the line, text font, coordinates of start and end points, and even what the text says, in the Properties panel of your Measurement module. For example, if you double click on "2D Length = 5000" in my example you would be able to change the text from "5000" to "5mm". This will update what's on the screen next to the scalebar.
5 - When everything looks good, you can take a screenshot by clicking on the camera button at the top of the screen.
How to export the individual labels from Avizo to MATLAB??
Is there an way that the processed files saved as.mat file so that the can be used for Matlab analysis.
I was using Avizo/Amira (both are available at a local HPC cluster) for biological FIB-SEM data processing, then found that Dragonfly is better for my tasks. Finally built a big PC (256 GB RAM, GPU Titan RTX 24 GB) at home during the Melbourne lockdown, and I'm very happy now - FIB-SEM stacks up to 80 GB (just don't have bigger) can be processed (including segmentation) without any problems. Thus, if someone is not happy with Avizo, I'd recommend to try Dragonfly, hope it is still free for academics.
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