Operating system: Ubuntu 16.04 LTS, MacOS 10.12.3
Slicer version: 4.6.2, also tested on 4.7.0 latest
Expected behavior: preserved transformed state when file opened outside Slicer including the entire volume of interest
Actual behavior: volume transformed but inappropriately cropped following resampling
This question builds on another thread I’ve found on the Slicer forum:
I have used the ACPC Transform module to align an image relative to the AC-PC plane in a brain volume (make it more symmetric). As a result, I have a transform matrix.
I first tried applying then hardening the transform and saving the volume (as .nii.gz format), but the transformation was not preserved (the output is identical to the input image). I followed the suggestion in the referenced thread and tried using the Resample Image (BRAINS) module with the following parameters:
- Image to Warp: original_volume
- Reference Image: none
- Output Image: transformed_volume
- Pixel Type: float
- Displacement Field (deprecated): None
- Transform file: ACPC transform
- Interpolation Mode: NearestNeighbor
All other settings were by default. After clicking apply, the volume appears transformed but is inappropriately cropped. I believe this is a result of not specifying a Reference Image (help text: “Reference image used only to define the output space. If not specified, the warping is done in the same space as the image to warp.”). I don’t have a reference image that matches the dimensions to be expected post-transform.
Any thoughts on how to resolve this problem?