Hi Luca,
Thanks for your help and the work you've put into it.
best,
david
On 19-07-13 16:59, Luca Antiga wrote:
Hello David,
the difference originates from the fact that vesselness was not scaled:
"Toggle scaling the objectness measure with the magnitude of the
largest absolute eigenvalue"
itkHessianToObjectnessMeasureImageFilter::ScaleObjectnessMeasure
I now added a flag in vmtkimagevesselenhancement
-scaled 0
or
-scaled 1
to toggle scaling off (the default) or on.
If you set it to 1 the output image will look a lot like Slicer's.
Note that you'll have to recompile vmtk from github.com/vmtk/vmtk
<http://github.com/vmtk/vmtk> to have this additional option available.
Best,
Luca
On Jul 16, 2013, at 10:37 AM, ddwilde wrote:
The imagecast gives the same result.
In the attachment is a (smaller) image dataset.
David
On 16-07-13 10:14, Luca Antiga wrote:
Yes, that's a marked difference indeed.
Have you tried casting the image to float?
vmtkimagecast -ifile CT.nii -type float --pipe
vmtkimagevesselenhancement -ofile vessel.nii -method frangi
-sigmamin 0.05 -sigmamax 0.25 -sigmasteps 5 -alpha 0.3 -beta 500
-gamma 150
Let me know, feel free to share your volume of interest (better
small than large).
Luca
On Jul 16, 2013, at 9:33 AM, ddwilde wrote:
Hi Luca,
Thanks for the reply.
However, the -stepmethod doesn't seem to be the problem. I've also
inspected the source code from the plugin and I still think that
all the parameters are the same. Is it maybe possible that the
difference occurs in the loading of the dataset (datatype=int16)?
To be more specific about the problem I've attached a screenshot of
the vmtk-slicer plugin and the vmtk results.
kind regards,
david
On 15-07-13 16:13, Luca Antiga wrote:
Hello David,
you can find the source code for the vesselness Slicer plugin here
https://github.com/haehn/VMTKSlicerExtension/blob/master/PythonModules/SlicerVmtkCommonLib/VesselnessFilteringLogic.py
I see that method for generating the steps is kept as the default
(for the C++ class), which is "logarithmic", while vmtk default is
"equispaced".
Try to specify
-stepmethod logarithmic
in the vmtk command line and see what happens.
Best,
Luca
On Jul 15, 2013, at 1:53 PM, ddwilde wrote:
Hi VMTK users,
I used the VMTK-plugin in Slicer4 to get a frangi vesselness
filtered
image of an angiografic CT image of a mouse dataset (with good
results).
However when I try to apply the same filter in VMTK directly
(with the
same parameters), I get different results. There appears to be a lot
more background noise. Is the definition of the parameters different
between both methods or am I doing something wrong?
Thanks,
David
Used parameters:
Slicer: Tube<-> Plates: 0.3 // Blobs <-> Tubes: 500 // Contrast:
150 //
minimum Diameter: 1[vx] // maximum Diameter: 5[vx]
VMTK: alpha: 0.3 // beta: 500 //
gamma: 150 // sigmamin: 0.05 [mm] // sigmamax : 0.25 [mm] //
sigmasteps: 5
VMTKcommand: vmtkimagevesselenhancement -ifile CT.nii -ofile
vessel.nii
-method frangi -sigmamin 0.05 -sigmamax 0.25 -sigmasteps 5 -alpha
0.3
-beta 500 -gamma 150
the image resolution is 0.05 mm
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