Paraview resample with dataset2/1/2024 If you want to visualize multi-terabyte images in Slicer then you can try the BigImage extension. You can also record and replay any node property changes (camera, slice views, display nodes, etc.) using Sequences module - but since keyframe animation is not available, this may not be an easy way to create animations. using Animation module in SlicerMorph extension. You can animate coming rendering properties, clipping, etc. but you may use volume rendering directly. If you can “segment” by just thresholding then you don’t need to go through segmentation, etc. It’s not as intuitive as adding a clipping plane in Paraview, but there might well be more direct ways to accomplish this task that I’ve not been able to find as I’m pretty new to Slicer. I could not find a simple way to do this with Slicer it seems that applying a clipping plane required me going through the segmentation editor, re-threshold the data to create a new segment, and then export segments as models to which I can finally apply a clipping plane. This is fairly standard stuff I’d imagine, but it also ties into some work we have in evaluating ParaView as a viable option for dealing with the visualization of large (i.e., multl-terabyte) data sets. The animations are fairly simply, and essentially involve moving clipping planes “revealing” certain aspects of multiple data sets in the same animation, likely with some additional rotations etc applied to move around the data sets during the animation(s). Cross-referencing with the original data is not required at that stage, fortunately! The output data is purely for visualization purposes, and so provided everything is consistent in the output files I can easily tweak the spacing etc in something like ParaView. I’m frustratingly close to having what I want here! As an option, sure -but as the default behaviour? I don’t see how it’s at all helpful!Ĭan I turn off that cropping, or do something to adjust the output from the “Resample Image (BRAINS)” functionality so this cropping does not happen? In any case, it’s really strange I’m not sure why people would want the output data to be cropped in this manner by default. I’m guessing this is because the image resampling crops the output to the bounding box of the “reference image” data, but I’m not sure about that. However: the very top of the resampled output file is chopped off! This actually seems to work, as the resampled output file is properly aligned with the target/fixed data as per the visual display in Slicer. I then tried the “Registration → Resample Image (BRAINS)” approach with “Image to Warp” as the second (i.e., moving) data set and “Reference Image” as the first (i.e., fixed) data set. Weirdly, this did actually seem to generate a resampled data set for the “fixed” target data (i.e., when I visualize the “old” and “new” versions of that data set in ParaView they are different), but the “moving” data set output is apparently identical to the input data set - just as if no transform(s) had been applied, or the data was not resampled. I therefore tried to use the Legacy → Filtering → Resample Scalar Volume menu option to generate a new (resampled) data set from each of my two aligned data sets. I understand that slicer does not resample the data by default, and so after applying the appropriate transform(s) if I simply save the data I won’t necessarily get the output that I expect. However, when trying to save the data I’m running into some problems. After hardening the transforms, the two (aligned) data sets look pretty good! I’ve got the alignment working via manual placement of three reference points on corresponding parts of the two data sets, and the alignment seems to work well. I then superpose the second data set onto the first (oriented) data set via the registration tools (Registration → Specialized → Fiducial Registration menu item). I first recentre the target data set volume on the world origin, and then tweak the orientation of that data to better align along the world axes. I’m trying to use Slicer 5.2.2 to align two 3D data sets, both of which feature data arranged on regular axis-aligned grid.
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