Re: [vmtk-users] vesselness filtering parameters

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

Hi David,
 thanks for the data, I'll take a look.

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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>>> 
>>> <slicer_plugin.png><vmtk.png>
>> 
> 
> <CT_voi.nii>