Sorry for the deluge of emails. I wasn't able to successfully get the
latest version of the VMTK source to run properly, so instead I just
downloaded the latest version of vmtkImageInitialization.py, which accepts
the parameters you specified.
My question is this: the description for the SourcePoints parameter is
"list of source point IJK coordinates". Am I able to specify more than one
SourcePoint and TargetPoint, and have it iterate over them? The alternative
would be to save the results to disk after each call and then merge them
all at the end before performing the LevelSetSegmentation, which seems
pretty hacky.
On Wed, Jun 26, 2013 at 11:07 AM, Richard Abrich <abri...@gmail.com> wrote:
> Hi again,
>
> I noticed that the latest version of VMTK in the Github repo has those
> parameters you specified. I'm currently compiling it, and will let you know
> how it goes.
>
> Thanks,
> Richard
>
>
>
> On Tue, Jun 25, 2013 at 5:37 PM, Richard Abrich <abri...@gmail.com> wrote:
>
>> 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 <abri...@gmail.com>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 <luca.ant...@orobix.com>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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>>>>
>>>
>>
>
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