[Rtk-users] Generating signal data from Amsterdam Shroud

Wed Sep 30 17:12:06 EDT 2015

Hi Matt,

Thank you so much for your help, again.

Unfortunately, I’m using windows system (windows7 64 with VS 2013) and I guess this could be a challenging issue to me.

Hi RTK users,

Is there anyone who successfully compiled RTK with “ITK + FFTW” in windows system?

I’m just trying to use rtkextractshroudsignal and it seems to require FFTW library externally.

When I tried to use FFTW 3.3.4, I’ve encountered link errors as shown below.

Any help will be highly appreciated.

Yang

From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] 
Sent: Wednesday, September 30, 2015 5:01 PM
To: Yang K Park <theday79 at gmail.com>
Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud

Yang,

I’m running on Ubuntu 14.04 LTS and used the distribution library (FFTW 3.3.3).  If you’re running on a Debian-based linux system, you can also install the full development library set using the following command: sudo apt-get install libfftw3-3 libfftw3-dev.  Then just make sure that these libraries are being used by rerunning CCMake.  

I’m not quite sure about the error being thrown in your build, but perhaps one of the main developers would be able to provide some more insight into the issue.

Hope this helps,

— Matt

__

Matthew J. Riblett
Virginia Commonwealth University
Department of Radiation Oncology
Medical Physics Graduate Program

Office:  Sanger Hall, Room B1-013

401 College Street   |  P.O. Box 980058

Richmond, Virginia 23298

VCU Email:                    riblettmj at vcu.edu <mailto:riblettmj at vcu.edu> 
MCV Office Phone:       +1.804.628.4858

On Sep 30, 2015, at 4:44 PM, Yang K Park <theday79 at gmail.com <mailto:theday79 at gmail.com> > wrote:

Hi Matt,

Thank you so much for your advice.

Recently I have revisited this project and tried to compile ITK with those options on as you suggested.

I’ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn’t work with RTK. 

There were some link errors like: 

rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter<class itk::Image<class std::complex<double>,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@?

May I ask you which version of fftw you are successfully using in which system(Windows or Linux)?

Thanks.

Yang

From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] 
Sent: Friday, September 18, 2015 6:56 PM
To: Yang K Park <theday79 at gmail.com <mailto:theday79 at gmail.com> >
Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud

Yang,

One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components.  This requires compilation with the ITK_USE_FFTWF and the

ITK_USE_FFTWD options.  I know, I didn’t compile that way initially, and it took a little bit of time to figure out.

Hope that helps,

— Matt

__

Matthew J. Riblett
Virginia Commonwealth University
Department of Radiation Oncology
Medical Physics Graduate Program

Office:  Sanger Hall, Room B1-013

401 College Street   |  P.O. Box 980058

Richmond, Virginia 23298

VCU Email:                     <mailto:riblettmj at vcu.edu> riblettmj at vcu.edu
MCV Office Phone:       +1.804.628.4858

On Sep 18, 2015, at 4:55 PM, Yang K Park < <mailto:theday79 at gmail.com> theday79 at gmail.com> wrote:

Hi Matt,

That sounds great! I really appreciate your advice.

I’m now compiling itk-4.8 to use that feature since I’ve found my itk version is a bit obsolete (4.4).

Thanks!

Yang

From: Matthew J. Riblett [ <mailto:riblettmj at mymail.vcu.edu> mailto:riblettmj at mymail.vcu.edu] 
Sent: Friday, September 18, 2015 4:31 PM
To: Yang K Park < <mailto:theday79 at gmail.com> theday79 at gmail.com>
Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud

Hi Yang,

Nice to hear from you!  I have had some success since my initial posting – in fact I’m currently working on a new method for accomplishing this task in certain challenging cases.

The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ‘-p’ flag at runtime:

rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA

>From what I’ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings.  Occasionally, I’ve run into issues where the default ‘unsharpness’ parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command).  On more challenging shroud images – notably, those with little detectable signal from background – additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction.

I hope that helps – and please let me know how it works out for you.

— Matt

__

Matthew J. Riblett
Virginia Commonwealth University
Department of Radiation Oncology
Medical Physics Graduate Program

Office:  Sanger Hall, Room B1-013

401 College Street   |  P.O. Box 980058

Richmond, Virginia 23298

VCU Email:                     <mailto:riblettmj at vcu.edu> riblettmj at vcu.edu
MCV Office Phone:       +1.804.628.4858

On Sep 18, 2015, at 4:12 PM, Yang K Park < <mailto:theday79 at gmail.com> theday79 at gmail.com> wrote:

Hi Matthew,

Hello, I found you in the RTK-thread.

Recently, I’ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue.

Thanks. 

Yang

_______________________________________________

Yang-Kyun Park, Ph.D., DABR

Assistant physicist & Instructor

Department of Radiation Oncology

Massachusetts General Hospital & Harvard Medical School

55 Fruit Street, Boston, MA 02114

Tel: +1-617-726-0186

Fax: +1-617-726-3603

From: Rtk-users [ <mailto:rtk-users-bounces at public.kitware.com> mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry
Sent: Tuesday, March 17, 2015 5:25 PM
To: Matthew J. Riblett < <mailto:riblettmj at mymail.vcu.edu> riblettmj at mymail.vcu.edu>
Cc:  <mailto:rtk-users at public.kitware.com> rtk-users at public.kitware.com
Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud

Hi Matthew, 

I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? 

Hope that helps,

Joel

On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < <mailto:riblettmj at mymail.vcu.edu> riblettmj at mymail.vcu.edu> wrote:

Hello fellow RTK users,

I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction.  I’ve been following along with the MC-CBCT Reconstruction example ( <http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction> http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished.  I’m trying to implement this into an automated workflow and I’d love to know how this was accomplished.

Thanks!

— Matt

__

Matthew J. Riblett
Virginia Commonwealth University
Department of Radiation Oncology
Medical Physics Graduate Program

Office:  Sanger Hall, Room B1-013

401 College Street   |  P.O. Box 980058

Richmond, Virginia 23298

VCU Email:      <mailto:riblettmj at vcu.edu> riblettmj at vcu.edu
MCV Office Phone:      <tel:%2B1.804.628.4858> +1.804.628.4858

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