Re: [vmtk-users] Command line parameters for vmtkLevelSetSegmentation

[Richard A. <ab...@gm...>]

Hi Luca,

Sorry I forgot to CC my last email to the mailing list.

A couple of addendums to my previous email (below):

1) I converted my data to the .mha format and am using the exact command
you suggested.

2) I used vmtk-exe.pyc instead of vmtk-exe.pyw in order to view the output.
The relevant lines seem to be:

Parsing options vmtkimageinitialization
vmtkimageinitialization error: unknown option -interactive

Just FYI, here is the revision information in the
vmtkimageinitialization.py script:

## Date:      $Date: 2006/05/31 10:51:21 $
## Version:   $Revision: 1.19 $

Is there a newer version I can grab from somewhere?


On Tue, Jun 25, 2013 at 5:13 PM, Richard Abrich <ab...@gm...> wrote:

> Hi Luca,
>
> Thanks so much for your help. I have a couple of questions:
>
> 1) My data isn't .mha format, but rather stored as a dicom set. I tried to
> do something like this instead:
>
> vmtkimagereader -f dicom -d C:/DICOM --pipe vmtkimageinitialization
> -interactive 0 -method collidingfronts -lowerthreshold 200.0 -sourcepoints
> 54 25 12 -targetpoints 89 60 24 --pipe vmtklevelsetsegmentation -iterations
> 200  -advection 1.0  -curvature 0.1  -propagation 0.0  -ofile C:/out.vtk
>
> However, the output file wasn't written, and I'm not sure how to check
> whether anything happened.
>
> 2) On a related note, I notice that in your example, you specify the ifile
> parameter for vmtklevelsetsegmentation again, even though you are piping
> the results from vmtkimageinitialization. Is this necessary? How can I do
> this using dicom sets instead?
>
> 3) A few of the parameters you specify for vmtkimagereader (e.g.
> interactive, method, lowerthreshold, sourcepoints, targetpoints) aren't
> listed in the documentation at
> http://www.vmtk.org/VmtkScripts/vmtkimageinitialization/ . I can see that
> LowerThreshold and UpperThreshold are properties of the
> vmtkImageInitialization object in vmtkImageInitialization.py, but the other
> parameters are a mystery. Where can I read more about them?
>
> Thanks again,
> Richard
>
>
> On Thu, Jun 20, 2013 at 4:41 PM, Luca Antiga <luc...@or...>wrote:
>
>> Hi Richard,
>>   indeed there is a way. The initialization phase in
>> vmtklevelsetsegmentation is performed by vmtkimageinitialization,
>> which accepts parameters at the command line and whose output can be
>> piped to vmtklevelsetsegmentation (in which
>> case the latter will use the initialized level sets generated by the
>> former). vmtklevelsetsegmentation can also run
>> non-interactively by specifying iterations and evolution parameters at
>> the command line. Here's a sample pipe:
>>
>> vmtkimageinitialization -ifile your_image_file.mha -interactive 0 -method
>> collidingfronts -lowerthreshold 200.0 -sourcepoints 54 25 12 -targetpoints
>> 89 60 24 --pipe vmtklevelsetsegmentation -ifile you_image_file.mha
>> -iterations 500 -advection 1.0 -curvature 0.1 -propagation 0.0 -ofile
>> level_set_file.mha
>>
>> One caveat: sourcepoints and targetpoints are in IJK coordinates (i.e.
>> voxel indices), not physical coordinates.
>>
>> Hope this helps,
>>
>>
>> Luca
>>
>>
>> On Jun 18, 2013, at 10:51 PM, Richard Abrich wrote:
>>
>> Hello,
>>
>> I'm interested in calling vmtkLevelSetSegmentation from a script. I want
>> to run colliding fronts with arbitrary thresholds and start/end position
>> vectors for the initial segmentation, and then run the level set
>> segmentation with arbitrary parameters.
>>
>> Unfortunately, there doesn't seem to be any way to specify these
>> parameters from the command line. What might be the easiest way to
>> accomplish this?
>>
>> Thanks,
>> Richard
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>