Hi!
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.
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 then superpose the second data set onto the first (oriented) data set via the registration tools (Registration → Specialized → Fiducial Registration menu item).
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. After hardening the transforms, the two (aligned) data sets look pretty good!
However, when trying to save the data I’m running into some problems.
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. 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. 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 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. 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. However: the very top of the resampled output file is chopped off!
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. 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. As an option, sure -but as the default behaviour? I don’t see how it’s at all helpful!
Can I turn off that cropping, or do something to adjust the output from the “Resample Image (BRAINS)” functionality so this cropping does not happen?
I’m frustratingly close to having what I want here!
Thanks!