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
>>>
>>> ------------------------------------------------------------------------------
>>> See everything from the browser to the database with AppDynamics
>>> Get end-to-end visibility with application monitoring from AppDynamics
>>> Isolate bottlenecks and diagnose root cause in seconds.
>>> Start your free trial of AppDynamics Pro today!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> vmtk-users mailing list
>>> vmtk-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>
>
> <slicer_plugin.png><vmtk.png>
------------------------------------------------------------------------------
See everything from the browser to the database with AppDynamics
Get end-to-end visibility with application monitoring from AppDynamics
Isolate bottlenecks and diagnose root cause in seconds.
Start your free trial of AppDynamics Pro today!
http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
_______________________________________________
vmtk-users mailing list
vmtk-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/vmtk-users
