Hi Hila,
assuming your blood vessels are perfectly straight and cylinder symmetrical
columns the smallest vessel which will not be removed by our implementation and
radius 1 has the following cross section:
XXX
XXX
XXX
Where each X is one voxel.
The exact volume of this depends on its orientation in regards to the
anisotropy. You can simulate this by creating a perfectly straight one voxel
column and dilating it by radius 1, eroding it again will give you the original
column.
Best,
Caspar
Von: Hila Hiler [mailto:[email protected]]
Gesendet: Mittwoch, 30. Mai 2012 12:19
An: Goch, Caspar Jonas
Cc: [email protected]
Betreff: Re: [mitk-users] opening with partial radius
a sharpened question:
if the 3D input image doesn't have isotropic dimensions (such as 0.5*0.5*1
mm^3)- which dimensions the structural element has (with radius 1, for example)?
if the answer is [0.5 0.5 1]=size(StrEle) it means that the opening process
will eliminate blood vessels with diameter 1*1*2 mm^3.
have I understood it right?
On Wed, May 30, 2012 at 1:16 PM, Goch, Caspar Jonas
<[email protected]<mailto:[email protected]>> wrote:
Hi Hila,
I am currently not aware of a direct out-of-the-box approach. But assuming you
have a binary segmentation and also assuming, that the small blood vessels you
have are basically a one voxel wide line (hence you trying to erode with 0.5)
you might for example go for eroding any voxel which has at least 20 zero value
voxels in a 26 neighborhood or something similar.
The itk neighborhood iterator might come in handy for this.
Best,
Caspar
Von: Hila Hiler [mailto:[email protected]<mailto:[email protected]>]
Gesendet: Mittwoch, 30. Mai 2012 11:45
An: Goch, Caspar Jonas
Cc: [email protected]<mailto:[email protected]>
Betreff: Re: [mitk-users] opening with partial radius
Hi Casper,
Thank you for the response.
Do you have any idea for an alternative way to do that ?
I just want to remove blood vessels which are smaller then 1mm.
Thanks in advance.
Hila
On Wed, May 30, 2012 at 12:34 PM, Goch, Caspar Jonas
<[email protected]<mailto:[email protected]>> wrote:
Hi Hila,
the radius you can set is used to construct an
itk::BinaryBallStructuringElement. The radius is not in millimeter but in a
voxel.
Best,
Caspar
Von: Hila Hiler [mailto:[email protected]<mailto:[email protected]>]
Gesendet: Mittwoch, 30. Mai 2012 08:43
An: [email protected]<mailto:[email protected]>
Betreff: Re: [mitk-users] opening with partial radius
correction:
if I want to erode with 1mm diameter (radius 0.5 as small blood vessels are) -
I can't do this with this tool?
On Tue, May 29, 2012 at 7:20 PM, Hila Hiler
<[email protected]<mailto:[email protected]>> wrote:
Hi all,
The basic image processing plug in is a very useful tool!
How ever, are the erosion/opening etc (unary manipulations) available only with
integers inputs (radius)?
if I want to erode with 1mm radius (as small blood vessels are) - I can't do
this with this tool?
Best Regards,
Hila
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