[Insight-users] Re: ITK Level Set Questions
Gaëtan Lehmann
gaetan.lehmann at jouy.inra.fr
Sat Oct 14 05:15:55 EDT 2006
Hi,
I think it should now be possible to create a subversion repository for a
contribution to the insight journal, so you can much easily work together,
if you want.
Julien, is the subversion capability of the insight journal ready ?
Thanks,
Gaetan
Le Sat, 14 Oct 2006 00:51:52 +0200, Benjamin Smith <brsmith at sfu.ca> a
écrit:
> 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
>> *********************************************
>>
--
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
http://voxel.jouy.inra.fr
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