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

Thu Sep 21 10:15:53 EDT 2017

Matlab is (was) a nice platform from algorithm prototyping, but implementing user interface in Matlab even for basic tasks, such as DICOM image import, reslicing, surface, volume visualization, etc. is a lot of work. I would recommend using 3D Slicer as user interface and running algorithms that you have implemented in Matlab using Slicer’s MatlabBridge (https://www.slicer.org/wiki/Documentation/Nightly/Extensions/MatlabBridge).

With growing popularity of Python and increasing number and quality of Python packages, Matlab is getting more and more irrelevant. I would recommend switching to Python as soon as you can. For example, you could easily put together algorithm prototypes that use ITK, as most (all?) ITK is already available in Python.

Andras

From: thanos thanos [mailto:thanosxania at gmail.com]
Sent: Thursday, September 21, 2017 9:58 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

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<mailto: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<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.slicer.org%2Fwiki%2FDocumentation%2FNightly%2FScriptRepository%23How_to_run_segment_editor_effects_from_a_script&data=02%7C01%7Classo%40queensu.ca%7C7daca75d4ffb4e3ab8c008d500f8d338%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636415991056644063&sdata=bLWnVZncZNGk0qLuK3lkVhjoFJMy23XTFXSisoRmkFU%3D&reserved=0>

How the rest of your pipeline is implemented (image loading, visualization, contouring, etc)?

Andras

From: thanos thanos [mailto:thanosxania at gmail.com<mailto:thanosxania at gmail.com>]
Sent: Thursday, September 21, 2017 8:22 AM
To: Andras Lasso <lasso at queensu.ca<mailto:lasso at queensu.ca>>
Cc: insight-users at itk.org<mailto: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<mailto: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<mailto:community-bounces at itk.org>] On Behalf Of thanos
Sent: Wednesday, September 20, 2017 10:21 AM
To: insight-users at itk.org<mailto: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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