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>
------------------------------------------------------------------------------
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