[ITK] [ITK-users] Cardiac Deformation using Segmentation and Registration of Ultrasound Images

Fri Sep 8 14:55:17 EDT 2017

FYI, a few weeks ago we added a nice 4D (3D+t) image registration extension to 3D Slicer. It works very well for cardiac volume sequences: it produces a motion-compensated volume sequence and a displacement field sequence.

Sequence Registration extension can be installed by a few clicks from the extension manager in recent 3D Slicer nightly versions. See more information and tutorial here: https://github.com/moselhy/SlicerSequenceRegistration

Andras

-----Original Message-----
From: Community [mailto:community-bounces at itk.org] On Behalf Of Matt McCormick
Sent: Friday, September 8, 2017 2:31 PM
To: thanos thanos <thanosxania at gmail.com>
Cc: insight-users at itk.org
Subject: Re: [ITK] [ITK-users] Cardiac Deformation using Segmentation and Registration of Ultrasound Images

Hello Thanos,

Yes, to add support for additional image formats, add the corresponding ITK module to the find_package(ITK COMPONENTS ... call:

  https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FInsightSoftwareConsortium%2FITKAnisotropicDiffusionLBR%2Fblob%2F50acf46da9fa1480eb502a0bb550c36d518893eb%2Fexamples%2FCMakeLists.txt%23L8&data=02%7C01%7Classo%40queensu.ca%7C3d7f50e0df534e04dfe708d4f6e7cd61%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636404922819639139&sdata=Vqviuh1be7etykTVE1mHIBzmrdv40KfVrsyinYJUKNw%3D&reserved=0

Thank you for the suggested correction to the usage documentation. It is added here:

  https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FInsightSoftwareConsortium%2FITKAnisotropicDiffusionLBR%2Fpull%2F12&data=02%7C01%7Classo%40queensu.ca%7C3d7f50e0df534e04dfe708d4f6e7cd61%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636404922819639139&sdata=uZf%2FlQ0EGne0tyyx6v58G%2Bqhh8jKJMgXE%2FYenk%2F4wls%3D&reserved=0

A Python package is now available for the module. It can be installed via

  python -m pip install --upgrade pip
  python -m pip install itk-anisotropicdiffusionlbr

Thanks,
Matt

On Mon, Aug 14, 2017 at 12:42 PM, thanos thanos <thanosxania at gmail.com> wrote:
> Hello again,
>
> Matt, thank you for solving the example issue. I tried to use the 
> filter and although it worked great for a 2D png image, it failed for 
> a 2D jpg and dicom images as well as for a 3D nrrd volume. I got the 
> error "Could not create ImageIO" so maybe that has to do with the ImageIOFactory.
>
> I liked the suggested and accepted values when I run the .exe but 
> maybe to avoid confusion you could replace the "Weickert diffusion 
> type. Accepted values: Edge, Coherence. Default: Edge."
> with
> Weickert diffusion type. Accepted values: EED cEED CED cCED Isotropic"
>
> Best regards,
> Thanos
>
> On Fri, Aug 11, 2017 at 6:55 PM, Matt McCormick 
> <matt.mccormick at kitware.com>
> wrote:
>>
>> On Fri, Aug 4, 2017 at 9:36 AM, Matt McCormick 
>> <matt.mccormick at kitware.com> wrote:
>> > Hi Thanos,
>> >
>> > On Thu, Aug 3, 2017 at 1:00 PM, thanos thanos 
>> > <thanosxania at gmail.com>
>> > wrote:
>> >> Hello everyone,
>> >>
>> >> Dženan, Andras and Matt thank you very much for your answers.
>> >> To be honest I've tried already in the past registration with 
>> >> Slicer using Demons, B-Splines and also Elastix and Plastimach.
>> >>
>> >> Dženan, I read your last sentence already many times but I can't 
>> >> really understand what you mean by "initializing registration of 
>> >> time point
>> >> n+1 by
>> >> resulting transform from time point n."
>> >>
>> >> Matt, thank you for sharing your thoughts. I already looked at the 
>> >> AnisotropicDiffusionLBR paper and I have also tried the online 
>> >> interactive figures
>> >>
>> >> (https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Finsightsoftwareconsortium.github.io%2FITKAnisotropicDiffusionLBR%2F&data=02%7C01%7Classo%40queensu.ca%7C3d7f50e0df534e04dfe708d4f6e7cd61%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636404922819639139&sdata=CYJJaN1M6zQUHs9HAlWipN2PrWEZlTL%2Fx4Ad%2FLVZMxk%3D&reserved=0).
>> >> Seems to work nicely, but I wasn't sure how to build the project. 
>> >> I already configured my ITK by setting the 
>> >> Module_AnisotropicDiffusionLBR at the CMake and then I tried to 
>> >> build the CoherenceEnhancingDiffusion from the 
>> >> C:\ITK\src\Modules\Remote\AnisotropicDiffusionLBR\examples but I got "
>> >> Cannot open include file: 'CoherenceEnhancingDiffusionFilter.h': 
>> >> No such file or directory " so I guess I am missing something..
>> >
>> > Thanks for the note. I will look into this issue and address it 
>> > next week.
>>
>> This is addressed here:
>>
>>   
>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Frevie
>> w.source.kitware.com%2F%23%2Fc%2F22567%2F&data=02%7C01%7Classo%40quee
>> nsu.ca%7C3d7f50e0df534e04dfe708d4f6e7cd61%7Cd61ecb3b38b142d582c4efb28
>> 38b925c%7C1%7C0%7C636404922819639139&sdata=XjWsPDq1Z%2BxvDcVUm9MFDDLa
>> BY%2BQHkuuuAgDhyKwQYg%3D&reserved=0
>>
>> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgith
>> ub.com%2FInsightSoftwareConsortium%2FITKAnisotropicDiffusionLBR%2Fcom
>> mit%2F3d9880d5f52c4c37e3b658abc607a13f3c3d9545&data=02%7C01%7Classo%4
>> 0queensu.ca%7C3d7f50e0df534e04dfe708d4f6e7cd61%7Cd61ecb3b38b142d582c4
>> efb2838b925c%7C1%7C0%7C636404922819639139&sdata=NN9XhKvMpJDHHL4DK1g2k
>> THZViGfwo6o%2B6wSOJAI7bo%3D&reserved=0
>>
>> I will also create a Python package for the module.
>>
>> Thanks,
>> Matt
>
>
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