Matching volume size with linear transformation

I have uCTscans of small frogs and we are trying to segment the hindlimb muscles for a study on locomotion. They were scanned in arbitrary orientations, which make it hard to identify the muscles. I would like to transform and save the volume in a standard orientation.

I have been able to apply a linear transform, however, when I try to resample the original volume with Resample scalar/vector/DWI volume while applying the linear transform, the resulting volume is now cropped.

It looks like I transformed the long, medium, and short axes of the volume but the volume remained defined in its original coordinate space, clipping part of the specimen. How do I rotate and resample the volume preserving the volume needed to capture the entire specimen? I tried entering Manual:size values (I assumed it was pixel numbers), but it did not make a difference. I did not change the spacing leaving it as 0,0,0.

Thank you for your help!

I would recommend to use “Crop volume” module for this. You can translate either the ROI node or the volume.