Re: [vmtk-users] vesselness filtering parameters

[Luca A. <luc...@or...>]

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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>> 
> 
> <slicer_plugin.png><vmtk.png>