I using 3D Slicer 4.10.2 to crop a CT abdominal Nifti volume for testing a deep learning model.
I have downloaded and installed the VolumeClip extension.
I select some options like Outside fill value = -1000, etc.
After clipping my input Nifti volume, to my heart’s content, I now wish to save it.
I then save 6 files, including the Nifti volume.
However, after I import the clipped Nifti volume into Fiji (Image/J),
the volume appears to be the original Nifti volume?
Is there any method to save the actual clipped volume in Nifti format?
Saved files contain what you see on screen. Normally you would have two volumes saved: the original and the clipped (same extents as the original, just some area blanked out).
If you want more elaborate tools for blanking out image regions, you can use Segment Editor module and “Surface cut” and “Mask volume” effects (provided by SegmentEditorExtraEffects extension).
If you want to reduce the image extents instead of blanking out regions then you can use Crop Volume module.