[Slicer For Fusion 360 Mac Download
Hanne Rylaarsdam
Hi everyone, I have only recently started using 3D Slicer and have a rather specific question:
I am trying to fuse the images of the same person head MRI and CT scans. I have tried the general registration (BRAINS) module, which works but the results are not yet satisfactory. Therefore I want to find out if this task is overall manageable and if so, what are the best ways/modules to do so?
Thanks
this is a very important registration step for instance in verifying the
results of DBS lead implantation by superimposing the postop CT onto the
preop T1 / T2 / SWI etc. However, none of the common registration method
work well (with the exception of Brainlab - but then, export and further
analysis with another tool is not possible). I tried flirt, ants, elastix
(SlicerElastix extension, as you suggested Andras), I think that the strong
contrast on the tissue-air-interface in CT causes the problem. I ended up
using landmark registration in MIPAV, but thats far from optimal.
Elastix worked really well for me for any reasonable registration problem that I threw at it. If you use a suitable metric (such as mutual information), then strong
contrast on the tissue-air-interface in CT should just help the registration . What kind of registration error did you have? Can you share a data set where you have registration issues?
Note that there are great rigid/affine/deformable landmark registration modules in Slicer. For images that are already somewhat aligned you can use Landmark registration module. For general cases, you can use Fiducial registration wizard module in SlicerIGT extension.
Do I understand correctly that you register pre/post-op images to each other by registering each to an atlas? That would not be ideal, as you need to register twice (instead of just once), and inter-patient (patient-to-atlas) registration is a much more difficult problem than intra-patient registration.
Yes, you understand correctly, I register pre and post op images to each
other, the postop images have the electrodes in them (which might be a part
of the problem). Is there a way to modify the parameters of elastix
directly in SlicerElastix or load a different parameter set other than the
presets?
To modify Elastix registration parameters, open Advanced section and click Show database folder button. It should show the registration preset database folder. You can edit ElastixParameterSetDatabase.xml to add new presets (name, description, etc. and a list of registration steps) and edit/add .txt files to edit registration steps.
Thank you, I had a look at the images and indeed registration is not trivial. Probably the best would be to do a literature review to see how others have approached this task before, but here are a few ideas that you may try:
Hi,
I have registered this kind of images and I tried the registration using
your data. After I increased the percentage of samples from 0.002 to 0.02
I got the results show in the attached screen capture. Is this registration
good enough or what kind of problems did you mean? I used General
Registration (BRAINS) modules of Slicer 4.8.
is it possible to make fusion of 3 studies (arterial, venous and late excretion phase in CT urography)? And than after the fusion where I will have arteries, veins and calices and ureters in one place to make segmentation of each part as done normally without fusion?
And I have issue with registration of the images.
When I want to chose moving image volume, only one study appears (bone CT scan), there is no MR study that I have loaded together with bone study as seen on the pic.fusion11196650 148 KB
Not sure exactly what you are asking regarding the cropping. You can crop the volumes either before or after transforming them. You might want to crop just the kidney to make registration more accurate and quicker.
You can display two frames at a time (one as background, another one as foreground volume) and fade between them. Basic Slicer visualization tutorials should cover this, but if not then let us know and we give step-by-step instructions.
I'm quite a long time a very happy autodesk user but it's my first post on the forum. Recently, a Slicer plugin / standalone for Fusion 360 was released. When checking out the plugin today, I was very happy to see finally something like this. I'm playing quite a lot with lasercutters, cnc mills etc. so I've been looking for this for a plugin like this for a while.
While testing the limits of the program, I discovered something weird. When scaling down the thickness of the sheet (I'd like to use 1,2mm cardboard), The program suddenly stopped slicing the model (it says: "Number of sheet generated is 0. Please change your manufacturing settings to fit model slices in stock dimensions"). I worked out the example of the humanhead.3dmk so you could try it yourself. When I duplicate the A4 size and downsize the thickness, it works just fine but I could not get any further than 0.025". So I hear you thinking, not a problem (it's 1mm) but I want to slice another model that's a lot higher and than this becomes already a problem when using much larger thicknesses.
Could it possibly be that there is some kind of upper limit of the number of parts / pages that the software could slice? Or is there any way of solving this problem because the resolution for my big model is really bad?
was this bug ever fixed? I just reinstalled the stand alone software and was still met with this obstacle thickness limitation. It is weird because the system seems to have assemble steps when my thickness is .001in ust not availble to be seen in sheets or as a pdf
Slices that display 0 sheets has not been fixed. One thing to try as a workaround is to rotate the slicing direction along the XY plane (so you would get the same slices anyways), which sometimes tends to fix the problem.
Stacked slices option seems to be problematic. The problem occurs when the model height is higher 8 centimeters and the material thickness lower than 4.5 mm. Playing around with the sectioning direction does not help for me.
I think I have found the solution for this problem. I used Autodesk Meshmixer to turn the stl mesh object in to a watertight solid body. It looks like the slicer properly functions this way.
Thanks everyone.
Arda
what helped me is to create a material, in my case it was A4 - 1,25mm thick cardboard I bought from Hobbycraft. I want to print it on my A4 printer and then glue sheets on cardboard and cut out with scalpel. After creating the material, save and close the file. Open it again, in my case it was from Fusion 360, and use the material you have just created. I had an issue with rotation of slices on the sheets so I changed size of A4 From 297 to 210 and 210 to 297 (portrait to landscape). And now I have no error with 0 sheets created. However, when I changed notch angle to 0, I am getting error message again.
I found another way, i needed to make 1,5mm slices, but it showed me the "0 sheet" problem. But it let me to do this work with 4,5mm slices, so I just scaled the model to make it 3 times biger, then I create the sheets and scale them back with an AutoCAD like software.
This may be an issue of how your computer rounds floats. I noticed the default sheet sizes were 0.1772" thick which is almost B flute thickness but not quite and using those sheets I did not get this error. I am planning on using 1/4" mdf for my project so I entered .25" as my thickness and got this "0 sheets" error. I then tried 0.2658 which is 0.1772 * 1.5 which successfully produced the sheets. The clue I got it actually looking at the default page sizes I saw values like 11.000004" which is the float approximation on 11 which is dependent on it being a double or not. I may not be right but I am going to go with compressing my object in the z axis by 94% in CAD and then slice in here.
I know there have been other posts about the Autodesk pulling the Slicer add-in from the app store, and that they are no longer supporting it. My question is what is everyone using as a replacement? Even though it has its bugs, I've still been using it, because its the easiest thing I can find to do what I need. I do a lot of EVA foam props, and use it to slice my models into layers that I then cut out of the foam and stack together to make the final prop. I have yet to find an alternative that's easy enough to use and gives me what I need. Is there other software packages that can accomplish the same thing? Or is there some process I could do in the manufacturing work space that I'm not aware of?
I've never used the manufacturing features in Fusion, but I'm not sure my workflow is exactly clear. Attached are some screen shots from the slicer stand alone version that still works. What I'm meaning to do is make a set of wearable claws out of EVA foam for a musical. The original "claw model.png" was created by editing a free file of a crab in Fusion to isolate just the claw, and brought into slicer, I then slice it on setting to replicate the sheets of 6mm thick EVA I use to generate the "sliced.png" model and the "patterns.png" to cut out the pieces to glue together. I've used this procedure several times with great success. If anything in the manufacturing environment can convert a model into sliced layers the way the slicer program can, I'd love to see a video tutorial on how to do it.
I'm also looking for a replacement to Slicer for Fusion 360 and/or info on whether it is compatible with Mac OS 11 (Big Sur). I use it for a number of projects and don't see anything else out there that does what I want in a simple way. In particular I've been using the radial function to create 3d terrain maps.
Thank you for putting together the video. I've never used "arrange" before. Unfortunately the work flow to get to that point is the issue. Most of the models I'm using aren't solid bodies. Instead I'm utilizing .stl or .obj files from sites like thingiverse or turbosquid. Those models come in as surfaces, which unfortunately can't be printed on a drawing to make the patterns I need. I can convert them to a solid, but then there's an issue where fusions limitation on how detailed the surface can be for conversion, I run into issues. Most of the time even if I slice the model into the layers I need (ranging between 4mm and 12mm thick due to foam thickness) to simplify them before converting them, the resulting geometry if very prismatic because to the way the surfaces are created. Which makes the patterns on the drawing very sloppy and inaccurate. Where as the independent slicer for fusion program works directly from the .stl or .obj and results in perfectly created patterns from the geometry. That's why I haven't really found a suitable replacement for the "slicer for fusion" program. The other program that people use alot for this type of work flow is pepakura, which basically takes a 3d model and converts it to a flat pattern kind of like what the sheet metal function does for a sheet metal piece. Which is fine for something like cosplay foam armor and so forth but again doesn't really work for me most of the time. I'd almost need to use something like a 3D printer or laser cutter slicer to generate the layers, but then there's no way of printing those to paper. And buying either type of machine to either cut them with a laser or pint thin pieces for a template isn't close to being in my budget at this time. That's why I'd LOVE to see the fusion slicer get supported again.
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