Hi,
I would like to know if there is a command (or a function in Aims librairies) for the "thinning" of a 3D shape :
- I have a 3D GIS image that contains an object extracted from an MRI.
- I have a template of this object which is 1-voxel wide
- I want to get the thin version (1-voxel wide) of my extracted object to allow registration with the template.
I suppose that the software I am currently using for this task extracts the skeleton of the object.
I know there are morphomath functions in Aims libraries, so if there is no Aims command for this, could you please explain how they work, so I can make the command myself ?
Thanks in advance,
Thinning
- Jean-Francois Mangin
- Posts: 337
- Joined: Mon Mar 01, 2004 10:24 am
- Location: Neurospin, CEA, France
- Contact:
I am afraid our thining algorithms are only hidden in Vip Commandlines...
Moreover, thinning is not a very robust operation. You have to pay attention to the topology of the initial object. The details of its boundaries may change the result a lot, depending on the thinning method. Finally the shape of the object may influence robustness a lot. In 3D, a flat object will reliably yield a flat skeleton, while a cylindric or spherical object may yield non controlledresults. We have a collegue here who spent some time playing with this for caudate, using Aims Library (Renaud Maroy). You may be interested getting in touch with him, even if this remains a difficult problem.
Moreover, thinning is not a very robust operation. You have to pay attention to the topology of the initial object. The details of its boundaries may change the result a lot, depending on the thinning method. Finally the shape of the object may influence robustness a lot. In 3D, a flat object will reliably yield a flat skeleton, while a cylindric or spherical object may yield non controlledresults. We have a collegue here who spent some time playing with this for caudate, using Aims Library (Renaud Maroy). You may be interested getting in touch with him, even if this remains a difficult problem.
- Jean-Francois Mangin
- Posts: 337
- Joined: Mon Mar 01, 2004 10:24 am
- Location: Neurospin, CEA, France
- Contact:
You could explore the possibilities of VipSkeleton, If you do not mind using a commandline. I am not sure of the best parameters, however, because this command is dedicated to the cortical fold pipeline. The good options may be missing.
Try something like
VipSkeleton -i frame -v n -c n
If it does not work, I may help you but not next week, I am not at work.
PS You may also get some help from Serge who played with this stuff during is PhD.
Try something like
VipSkeleton -i frame -v n -c n
If it does not work, I may help you but not next week, I am not at work.
PS You may also get some help from Serge who played with this stuff during is PhD.
Thanks a lot !
The results I get with
look like the image I expected.
I still have to check that my other programs work correctly with the computed skeleton.
The results I get with
Code: Select all
VipSkeleton -i frame.ima -v n -c n -sk s
I still have to check that my other programs work correctly with the computed skeleton.
Manik Bhattacharjee
INSERM U836
INSERM U836