Re: [vmtk-users] vesselness filtering parameters

[ddwilde <dav...@ug...>]

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