Hi Yan,

Convert3D does not know, of course, where the left and right side of the brain is situated, but if you identify the voxel coordinates of the sagittal midline, you can define a subvolume to crop the image to using the -region command:


The above coordinates are my best estimate for the midline (see attached image for the cropping results - I tested this on the v3 atlas volume, but it works the same way for version 4, of course).

For details on the -region command, please see https://sourceforge.net/p/c3d/git/ci/master/tree/doc/c3d.md#-region-extract-region-from-image

While looking for this, I found an alternative command for splitting an image volume to individual labels, that may be of interest to you (may be faster if you need all regions):
https://sourceforge.net/p/c3d/git/ci/master/tree/doc/c3d.md#-split-split-multi-label-image-into-binary-images

All the best,
Eszter