[ITK] [ITK-users] New Submission: ND morphological contour interpolation

Thu Sep 21 09:58:21 EDT 2017

Thank you for your reply!
I have some binary data which I load in Matlab and I reshape them to obtain
my 3D image. I perform 2D semi-automatic segmentation (based on active
contours and b-splines) where I obtain both the curve as a set of points as
well as binary images which I then multiple with my original image. I then
use isosurfaces to get the 3D model.
What I want is to avoid performing the semi-automatic segmentation on each
slice so I thought of creating a binary 3D model with missing slices and
then do the interpolation. I will study now the "grow from seeds effect"
and working with scripts on Slicer since I haven't done this before..

Best,
Thanos

On Thu, Sep 21, 2017 at 3:27 PM, Andras Lasso <lasso at queensu.ca> wrote:

> It should be easy to write an executable like that. It can be either a
> standalone executable, or – if you want to use other effects or you don’t
> want to set up a build environment on multiple platforms and create
> distribution mechanism (software download page and/or app store) – then you
> can do it using 3D Slicer and a small Python script. See for example how to
> apply a Segment Editor effect in a script here:
> https://www.slicer.org/wiki/Documentation/Nightly/
> ScriptRepository#How_to_run_segment_editor_effects_from_a_script
>
>
>
> How the rest of your pipeline is implemented (image loading,
> visualization, contouring, etc)?
>
>
>
> Andras
>
>
>
> *From:* thanos thanos [mailto:thanosxania at gmail.com]
> *Sent:* Thursday, September 21, 2017 8:22 AM
> *To:* Andras Lasso <lasso at queensu.ca>
> *Cc:* insight-users at itk.org
>
> *Subject:* Re: [ITK] [ITK-users] New Submission: ND morphological contour
> interpolation
>
>
>
> Hello Andras,
>
>
>
> Thank you very much for your answer. I already tried Slicer and the
> Segment Editor and it works fine. I was wondering if I can make an
> executable that I could use for my data (for example an .nrrd segmented
> volume with some slices missing).
>
>
>
> Best regards,
>
> Thanos
>
>
>
> On Wed, Sep 20, 2017 at 6:25 PM, Andras Lasso <lasso at queensu.ca> wrote:
>
> If you want to see what the morphological contour interpolation filter can
> do, then download nightly version of 3D Slicer (www.slicer.org
> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.slicer.org&data=02%7C01%7Classo%40queensu.ca%7Ca08e625765f04a0fac1408d500eb5119%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636415933050412732&sdata=ADd9uXu9%2FX%2BkJr5FW1P1vKgLtvzgpx8b8tQtel%2FWgE4%3D&reserved=0>)
> and try "Fill between slices" effect. Some information about the tool is
> available at  http://slicer.readthedocs.io/en/latest/user_guide/module_
> segmenteditor.html
> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fslicer.readthedocs.io%2Fen%2Flatest%2Fuser_guide%2Fmodule_segmenteditor.html&data=02%7C01%7Classo%40queensu.ca%7Ca08e625765f04a0fac1408d500eb5119%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636415933050412732&sdata=Dz2kfKpmJrib0je7bRayRVmqmCTLvmAbnQUL6eu92sU%3D&reserved=0>,
> but if you are stuck at any point then you can ask help at
> https://discourse.slicer.org
> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdiscourse.slicer.org&data=02%7C01%7Classo%40queensu.ca%7Ca08e625765f04a0fac1408d500eb5119%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636415933050412732&sdata=SWrqY0hKYfYPc7UhOP%2FuAjl2WZDM%2F2pgEusdpmNG1Pk%3D&reserved=0>
> - all questions are answered, typically within a few hours.
>
> Andras
>
> -----Original Message-----
> From: Community [mailto:community-bounces at itk.org] On Behalf Of thanos
> Sent: Wednesday, September 20, 2017 10:21 AM
> To: insight-users at itk.org
> Subject: Re: [ITK] [ITK-users] New Submission: ND morphological contour
> interpolation
>
> Hello,
>
> Is there maybe an example for the morphological contour interpolation?
> I am working on Matlab for the segmentation of some 3D data and since I am
> currently segmenting semi-automatically slice by slice, it would be great
> if I could use this class..
> I also have a quite silly question.. I am aware about the "test" folder
> and data but I don't really understand what is used for... I had a look on
> the Software Guide on the chapter "How to create a module" but I still
> don't get it..
>
> Thank you very much.
>
> Best regards,
> Thanos
>
>
>
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