[Insight-users] Re: ITK Level Set Questions
Benjamin Smith
brsmith at sfu.ca
Fri Oct 13 18:51:52 EDT 2006
Hello Nawel,
I am actually just starting to implement some of the Chan-Vese papers using
ITK myself. Please feel free to contact me, and perhaps we can help each
other work through our respective implementations.
Cheers
Ben
On 10/13/06, insight-users-request at itk.org <insight-users-request at itk.org>
wrote:
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> Today's Topics:
>
> 1. Re: I need help (garzo)
> 2. Re: I need help (garzo)
> 3. Re: Talairach Normalization (Vladimir FONOV)
> 4. RE: Getting at private dicom tags (Kris Thielemans)
> 5. Re: ITK Level Set Questions (nawel h)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 12 Oct 2006 11:25:08 -0700 (PDT)
> From: garzo <adrian_prieto_jimenez at hotmail.com>
> Subject: Re: [Insight-users] I need help
> To: insight-users at itk.org
> Message-ID: <6781854.post at talk.nabble.com>
> Content-Type: text/plain; charset=UTF-8
>
>
> -First:
>
> Thank you very much for your help. I used CMake correctly with ITK
> (without
> errors or warnings)
>
> -Second:
>
> Now, when I try to use "make" in the BIN directory of my ITK, 1 error and
> 2
> warnings happen (after that the system works 1 or 2 minutes):
>
> ******************************************************************
> C:\itk\src\InsightToolkit-2.8.1\Utilities\gdcm\src\gdcmVR.cxx:
> Error E2285 C:\itk\src\InsightToolkit-2.8.1\Utilities\gdcm\src\gdcmVR.cxx
> 122: C
> ould not find a match for 'std::binary_search<ForwardIterator,T>(const
> std::stri
> ng *,const std::string *,const std::string)' in function
> VR::IsVROfStringReprese
> ntable(const std::string &)
> Warning W8004 C:\itk\src\InsightToolkit-
> 2.8.1\Utilities\gdcm\src\gdcmVR.cxx
> 123:
> 'end' is assigned a value that is never used in function
> VR::IsVROfStringRepres
> entable(const std::string &)
> Warning W8057 C:\itk\src\InsightToolkit-
> 2.8.1\Utilities\gdcm\src\gdcmVR.cxx
> 123:
> Parameter 'tested' is never used in function
> VR::IsVROfStringRepresentable(cons
> t std::string &)
> *** 1 errors in Compile ***
>
> ** error 1 ** deleting
> Utilities\gdcm\src\CMakeFiles\itkgdcm.dir\gdcmVR.obj
>
> ** error 1 ** deleting Utilities\gdcm\src\CMakeFiles\itkgdcm.dir\all
>
> ** error 1 ** deleting all
> ********************************************************************
>
> What can I do now?
>
> Thanks.
>
> Adrian Prieto.
>
>
> Luis Ibanez wrote:
> >
> >
> > Hi Garzo,
> >
> > It may seem that your Borland compiler
> > has not been configured correctly
> >
> > Please take a look at the following instructions:
> > http://community.borland.com/article/0,1410,21205,00.html
> >
> > In particular the second part: "Creating the configuration files"
> > where you have to create the files:
> >
> >
> > ILINK32.CFG
> > BCC32.CFG
> >
> >
> > Please let us know if that help,
> >
> >
> > Thanks
> >
> >
> > Luis
> >
> >
> > --------------------
> > Garzo Garzo wrote:
> >> Hi,
> >>
> >> I´m trying to build ITK in my Computer, but I can´t... I don´t know
> what
> >> is going wrong... I need help.
> >>
> >> My System has:
> >>
> >> -Windows XP
> >> -Borland C++ Compiler 5.5
> >> -Cmake 2.2
> >> -InsightToolkit-2.8.1 (without build, of course)
> >>
> >> My steps were the next:
> >>
> >> 1º: I configure the PATH variable with the Borland 5.5 address
> >> (C:\Borland\BCC55\Bin)
> >> 2º: I create a Binary and a Source Folder ("C:\itk\src\" and
> >> "C:\itk\bin\")
> >> 3º: I copy "InsightToolkit-2.8.1" in the Source folder
> >> ("C:\itk\src\InsightToolkit-2.8.1")
> >> 4º: I install Cmake 2.2
> >> 5º: I run Cmake 2.2
> >> 6º: I select "C:\itk\src\InsightToolkit-2.8.1" for SOURCE CODE and
> >> "C:\itk\bin\" for BINARIES
> >> 7º: I press the "Configure" button
> >> 8º: And then a Error Message success (The ErrorMessage is too big, I
> >> write only the "error" part):
> >>
> >> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> ........
> >> ........
> >> Borland C++ 5.5 for Win32 Copyright (c) 1993, 2000 Borland
> >> Turbo Incremental Link 5.00 Copyright (c) 1997, 2000 Borland
> >> Fatal: Unable to open file 'C0X32.OBJ'
> >>
> >> ** error 1 ** deleting cmTryCompileExec.exe
> >> ** error 1 ** deleting CMakeFiles\cmTryCompileExec.dir\all
> >> ** error 1 ** deleting CMakeFiles\cmTryCompileExec.dir\rule
> >> ** error 1 ** deleting cmTryCompileExec
> >>
> >> CMake will not be able to correctly generate this project.
> >>
> >> (Press Cancel to suppress any further messages.)
> >> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>
> >> May you help me, please?
> >>
> >> Thanks.
> >>
> >> P.D: if you need more info about the ErrorMessage, I can write all the
> >> message.
> >>
> >> _________________________________________________________________
> >> Descubre la descarga digital con MSN Music. Más de un millón de
> >> canciones. http://music.msn.es/
> >>
> >> _______________________________________________
> >> Insight-users mailing list
> >> Insight-users at itk.org
> >> http://www.itk.org/mailman/listinfo/insight-users
> >>
> >>
> >
> >
> > _______________________________________________
> > Insight-users mailing list
> > Insight-users at itk.org
> > http://www.itk.org/mailman/listinfo/insight-users
> >
> >
>
> --
> View this message in context:
> http://www.nabble.com/I-need-help-tf2414777.html#a6781854
> Sent from the ITK - Users mailing list archive at Nabble.com.
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 12 Oct 2006 11:30:16 -0700 (PDT)
> From: garzo <adrian_prieto_jimenez at hotmail.com>
> Subject: Re: [Insight-users] I need help
> To: insight-users at itk.org
> Message-ID: <6781948.post at talk.nabble.com>
> Content-Type: text/plain; charset=UTF-8
>
>
> I don´t know if this info is important or not for my new problem, but I
> configured CMake Cache Values like this:
>
> BUILD_EXAMPLES = ON
> BUILD_SHARED_LIBS = OFF
> BUILD_TESTING = ON
>
> Thanks another time.
>
> Adrian Prieto.
>
>
> garzo wrote:
> >
> > -First:
> >
> > Thank you very much for your help. I used CMake correctly with ITK
> > (without errors or warnings)
> >
> > -Second:
> >
> > Now, when I try to use "make" in the BIN directory of my ITK, 1 error
> and
> > 2 warnings happen (after that the system works 1 or 2 minutes):
> >
> > ******************************************************************
> > C:\itk\src\InsightToolkit-2.8.1\Utilities\gdcm\src\gdcmVR.cxx:
> > Error E2285 C:\itk\src\InsightToolkit-
> 2.8.1\Utilities\gdcm\src\gdcmVR.cxx
> > 122: C
> > ould not find a match for 'std::binary_search<ForwardIterator,T>(const
> > std::stri
> > ng *,const std::string *,const std::string)' in function
> > VR::IsVROfStringReprese
> > ntable(const std::string &)
> > Warning W8004
> > C:\itk\src\InsightToolkit-2.8.1\Utilities\gdcm\src\gdcmVR.cxx 123:
> > 'end' is assigned a value that is never used in function
> > VR::IsVROfStringRepres
> > entable(const std::string &)
> > Warning W8057
> > C:\itk\src\InsightToolkit-2.8.1\Utilities\gdcm\src\gdcmVR.cxx 123:
> > Parameter 'tested' is never used in function
> > VR::IsVROfStringRepresentable(cons
> > t std::string &)
> > *** 1 errors in Compile ***
> >
> > ** error 1 ** deleting
> > Utilities\gdcm\src\CMakeFiles\itkgdcm.dir\gdcmVR.obj
> >
> > ** error 1 ** deleting Utilities\gdcm\src\CMakeFiles\itkgdcm.dir\all
> >
> > ** error 1 ** deleting all
> > ********************************************************************
> >
> > What can I do now?
> >
> > Thanks.
> >
> > Adrian Prieto.
> >
> >
> > Luis Ibanez wrote:
> >>
> >>
> >> Hi Garzo,
> >>
> >> It may seem that your Borland compiler
> >> has not been configured correctly
> >>
> >> Please take a look at the following instructions:
> >> http://community.borland.com/article/0,1410,21205,00.html
> >>
> >> In particular the second part: "Creating the configuration files"
> >> where you have to create the files:
> >>
> >>
> >> ILINK32.CFG
> >> BCC32.CFG
> >>
> >>
> >> Please let us know if that help,
> >>
> >>
> >> Thanks
> >>
> >>
> >> Luis
> >>
> >>
> >> --------------------
> >> Garzo Garzo wrote:
> >>> Hi,
> >>>
> >>> I´m trying to build ITK in my Computer, but I can´t... I don´t know
> what
> >>> is going wrong... I need help.
> >>>
> >>> My System has:
> >>>
> >>> -Windows XP
> >>> -Borland C++ Compiler 5.5
> >>> -Cmake 2.2
> >>> -InsightToolkit-2.8.1 (without build, of course)
> >>>
> >>> My steps were the next:
> >>>
> >>> 1º: I configure the PATH variable with the Borland 5.5 address
> >>> (C:\Borland\BCC55\Bin)
> >>> 2º: I create a Binary and a Source Folder ("C:\itk\src\" and
> >>> "C:\itk\bin\")
> >>> 3º: I copy "InsightToolkit-2.8.1" in the Source folder
> >>> ("C:\itk\src\InsightToolkit-2.8.1")
> >>> 4º: I install Cmake 2.2
> >>> 5º: I run Cmake 2.2
> >>> 6º: I select "C:\itk\src\InsightToolkit-2.8.1" for SOURCE CODE and
> >>> "C:\itk\bin\" for BINARIES
> >>> 7º: I press the "Configure" button
> >>> 8º: And then a Error Message success (The ErrorMessage is too big, I
> >>> write only the "error" part):
> >>>
> >>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>> ........
> >>> ........
> >>> Borland C++ 5.5 for Win32 Copyright (c) 1993, 2000 Borland
> >>> Turbo Incremental Link 5.00 Copyright (c) 1997, 2000 Borland
> >>> Fatal: Unable to open file 'C0X32.OBJ'
> >>>
> >>> ** error 1 ** deleting cmTryCompileExec.exe
> >>> ** error 1 ** deleting CMakeFiles\cmTryCompileExec.dir\all
> >>> ** error 1 ** deleting CMakeFiles\cmTryCompileExec.dir\rule
> >>> ** error 1 ** deleting cmTryCompileExec
> >>>
> >>> CMake will not be able to correctly generate this project.
> >>>
> >>> (Press Cancel to suppress any further messages.)
> >>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>>
> >>> May you help me, please?
> >>>
> >>> Thanks.
> >>>
> >>> P.D: if you need more info about the ErrorMessage, I can write all the
> >>> message.
> >>>
> >>> _________________________________________________________________
> >>> Descubre la descarga digital con MSN Music. Más de un millón de
> >>> canciones. http://music.msn.es/
> >>>
> >>> _______________________________________________
> >>> Insight-users mailing list
> >>> Insight-users at itk.org
> >>> http://www.itk.org/mailman/listinfo/insight-users
> >>>
> >>>
> >>
> >>
> >> _______________________________________________
> >> Insight-users mailing list
> >> Insight-users at itk.org
> >> http://www.itk.org/mailman/listinfo/insight-users
> >>
> >>
> >
> >
>
> --
> View this message in context:
> http://www.nabble.com/I-need-help-tf2414777.html#a6781948
> Sent from the ITK - Users mailing list archive at Nabble.com.
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 12 Oct 2006 14:10:12 -0400
> From: Vladimir FONOV <vladimir.fonov at gmail.com>
> Subject: [Insight-users] Re: Talairach Normalization
> To: insight-users at itk.org
> Message-ID: <egm0e5$ob6$1 at sea.gmane.org>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> advanced math wrote:
> >
> > Does anybody know any software which can perform Talairach
> > Normalization of the MRI volume data?
> > Thank you.
> >
> Minc software can do talairach-like normalization:
> http://www.bic.mni.mcgill.ca/software/
>
> The process described here:
> http://wiki.bic.mni.mcgill.ca/index.php/mni_autoreg , all software is
> available at http://packages.bic.mni.mcgill.ca/ . There are sources at
> http://packages.bic.mni.mcgill.ca/tgz/ and precompiled packages
> for Debian Linux: http://packages.bic.mni.mcgill.ca/deb/
> for Mac OS X : http://packages.bic.mni.mcgill.ca/osx
> and for Cygwin there is one big package which includes all the tools:
> http://packages.bic.mni.mcgill.ca/cygwin/mni_cygwin_tar-1.3.tar.gz
>
> + You would need models :
> http://packages.bic.mni.mcgill.ca/tgz/mni-models_icbm152-lin-1.0.tar.gz
>
>
> P.S. This would imply that you will have to convert your data into minc
> data format.
> --
> Best regards,
> Vladimir S. Fonov ~ vladimir dot fonov at gmail dot com
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 13 Oct 2006 10:05:34 +0100
> From: "Kris Thielemans" <kris.thielemans at csc.mrc.ac.uk>
> Subject: [Insight-users] RE: Getting at private dicom tags
> To: "'Kris Thielemans'" <kris.thielemans at csc.mrc.ac.uk>,
> <insight-users at itk.org>
> Message-ID: <003601c6eea6$be2efc90$0d0a10ac at bach>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi
>
>
>
> I solved my own problem (original post of 1 month ago quoted below). I
> just
> thought to let you know.
>
> The bit that I didn't tell you was that I had to read one of the files in
> the series to get at the value of the tags, which I do as follows:
>
> typedef itk::GDCMImageIO ImageIOType;
> ImageIOType::Pointer dicomIO = ImageIOType::New();
> typedef itk::Image< float, 2 > ImageType2D;
> typedef itk::ImageFileReader< ImageType2D > ReaderType2D;
> ReaderType2D::Pointer reader = ReaderType2D::New();
> reader->SetImageIO( dicomIO );
> typedef std::vector<std::string> FileNamesContainer;
> FileNamesContainer fileNames =
> nameGenerator->GetFileNames( seriesItr->c_str());
> reader->SetFileName( fileNames[0].c_str() );
> reader->Update();
>
> Only then can I call dicomIO->GetMetaDataDictionary() as I said in my
> original post.
>
> So, where was the problem?
>
> I had set
> nameGenerator->SetLoadPrivateTags ( true );
>
> But I had NOT set
> dicomIO->SetLoadPrivateTags(true);
>
> I guess I thought that this was done by the nameGenerator business but as
> that one doesn't know about dicomIO, that was rather stupid.
>
> Now you know.
>
> Kris
>
> > -----Original Message-----
> > From: Thielemans, Kris [mailto:kris.thielemans at imperial.ac.uk]
> > Sent: 15 September 2006 18:07
> > To: insight-users at itk.org
> > Subject: Getting at private dicom tags
> >
> > Hi
> >
> > I need to get the value of a private tag (frame number in GE gated PET
> > data). I know for sure that the tag is there (for instance using
> > dcmtk's dcmdump).
> >
> > I've modified the example IO/DicomSeriesReadPrintTags to what's
> > happening, e.g. I've added
> >
> > nameGenerator->SetLoadPrivateTags ( true );
> > nameGenerator->AddSeriesRestriction("0009|10D8" );
> >
> > This works in the sense that the value of the frame_number now gets
> > added to the 'seriesIdentifier'. However, when I try to get at its
> > value using
> >
> > typedef itk::MetaDataDictionary DictionaryType;
> > const DictionaryType & dictionary =
> > dicomIO->GetMetaDataDictionary();
> > DictionaryType::ConstIterator tagItr = dictionary.Find( "0009|10D8"
> > );
> >
> > this function tells me that it cannot find the tag. (It can find some
> > e.g. "0020|0011" SeriesNumber or patientName.
> >
> > Indeed, the output of (my modified) DicomSeriesReadPrintTags shows no
> > private tags.
> >
> > Is there a way around this?
> >
> > Thanks
> >
> > Kris Thielemans
> > Hammersmith Imanet, part of GE Healthcare
> >
>
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 13 Oct 2006 11:36:25 +0200
> From: "nawel h" <nawel_h5 at hotmail.com>
> Subject: [Insight-users] Re: ITK Level Set Questions
> To: insight-users at itk.org
> Message-ID: <BAY108-F210C81597E8CD4F34D7401BC0A0 at phx.gbl>
> Content-Type: text/plain; charset=iso-8859-1; format=flowed
>
> Hi
> I was wondering if there hasn't been any answers to the mail of Pingkun. I
> didn't find anything on the web and I am plannig to implement the
> multi-phase Level Set of Chan and Vese
> Thanks in advance!
> nawel
>
> >Hi Luis,
> >
> >Can you give some suggestions on implementing multi-phase level sets
> >based on current itk level set methods?
> >
> >I think the most naive approach may be evolving several active
> >contours (embedded in different level set maps) simultaneously and
> >minimizing the overlapping areas between them. What do you think of
> >it?
> >
> >Pingkun
>
>
>
>
> ------------------------------
>
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users
>
>
> End of Insight-users Digest, Vol 30, Issue 25
> *********************************************
>
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