here is a short and easy-to-understand example. The input is an image with
interpolated. If smoothing radius is provided, it is used. I will test this
a bit more and integrate into the repository, per Matt's suggestion.
Post by Andras LassoMatlab 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 Slicerâs 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
*Sent:* Thursday, September 21, 2017 9:58 AM
*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
It should be easy to write an executable like that. It can be either a
standalone executable, or â if you want to use other effects or you donât
want to set up a build environment on multiple platforms and create
distribution mechanism (software download page and/or app store) â then you
can do it using 3D Slicer and a small Python script. See for example how to
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
*Sent:* Thursday, September 21, 2017 8:22 AM
*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
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-----
Sent: Wednesday, September 20, 2017 10:21 AM
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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