Using a scaled down version of a volume to segment, then using this segment on original large size volumes

Dear all,
I have large datasets (10 to 30GB per image) which are thus difficult to segment on original files. One solution I imagined is
1- to use a 10X downscaled version of my images,
2- paint “seeds” in the 14 regions I want segmented,
3- shrink the sizes of each segment by a couple of voxels,
4- then apply the seg.nrrd file to the original large size image after and
5- apply a grow from seed function (and go make myself a coffee…).
Everything works well up to step 5. Segments are matching to the new high resolution image but are somewhat fixed to low resolution settings.

Thanks for your help

Apologies for posting something I eventually found a solution for.
I needed to edit the Specify Geometry option to oversampling the seg.nrrd file and increase it 10X
I am now running grow from seed the way it is supposed to on high resolution images.
Kind regards (and if moderators feel this is not a useful topic, feel free to delete)

Thanks for posting this - yes, we definitely like to keep this kind of post in the system so that others can learn in the future.

1 Like