[Insight-users] Dice Similarity Coefficient in ITK?
Ross, James C (GE, Research)
ross at crd.ge.com
Wed May 28 10:37:44 EDT 2008
Dan,
You might also take a look at itkKappaStatisticImageToImageMetric.
-James
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Today's Topics:
1. Relative maximums (Irene Gonz?lvez Garc?a)
2. Re: Relative maximums (Xabier Artaechevarria Artieda)
3. Re: Relative maximums (Luis Ibanez)
4. Re: Relative maximums (Ga?tan Lehmann)
5. Re: Wrap IKT repeats wrapping during make install?
(Ga?tan Lehmann)
6. Dice Similarity Coefficient in ITK? (Blezek, Daniel J., Ph.D.)
7. Re: [Insight-developers] Dice Similarity Coefficient in ITK?
(Karthik Krishnan)
8. Cannot change the series description (0008|103E) of a dicom
file using ITK (andreasfm at web.de)
9. Re: [Insight-developers] ITK factory, MacOSX, .so, .dylib
(Bill Hoffman)
10. Re: [Insight-developers] ITK factory, MacOSX, .so, .dylib
(Bill Lorensen)
----------------------------------------------------------------------
Message: 1
Date: Tue, 27 May 2008 18:59:46 +0200
From: Irene Gonz?lvez Garc?a <irenegonzalvezg at gmail.com>
Subject: [Insight-users] Relative maximums
To: insight-users at itk.org
Message-ID: <483C3E02.3060303 at gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Dear all,
I would like to know if there is any method where I can calculate all
the relative maximums in a 3D image and then, with these points
(relative maximums) create a new image.
Thanks for your help
Best regards
Irene
------------------------------
Message: 2
Date: Tue, 27 May 2008 19:08:41 +0200
From: Xabier Artaechevarria Artieda <xabiarta at unav.es>
Subject: Re: [Insight-users] Relative maximums
To: insight-users at itk.org
Message-ID: <20080527190841.7jltlgpdicss0ksg at webmail.unav.es>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
format="flowed"
Hi Irene,
This filter might do what you are looking for:
http://www.itk.org/Doxygen34/html/classitk_1_1HConvexImageFilter.html
Best regards,
Xabi
--
Xabier Artaechevarria
Cancer Imaging Laboratory
Centre for Applied Medical Research
www.cima.es
Irene Gonz?lvez Garc?a <irenegonzalvezg at gmail.com> ha escrito:
> Dear all,
> I would like to know if there is any method where I can calculate all
> the relative maximums in a 3D image and then, with these points
> (relative maximums) create a new image.
>
> Thanks for your help
> Best regards
> Irene
>
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users
----------------------------------------------------------------
Este mensaje ha sido enviado desde https://webmail.unav.es
------------------------------
Message: 3
Date: Tue, 27 May 2008 13:47:11 -0400
From: Luis Ibanez <luis.ibanez at kitware.com>
Subject: Re: [Insight-users] Relative maximums
To: Irene Gonz?lvez Garc?a <irenegonzalvezg at gmail.com>
Cc: insight-users at itk.org
Message-ID: <483C491F.1010802 at kitware.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Irene,
In addition to Xabier's suggestion,
You may also want to look at:
http://www.itk.org/Insight/Doxygen/html/classitk_1_1RegionalMaximaImageF
ilter.html
Regards,
Luis
--------------------------
Irene Gonz?lvez Garc?a wrote:
> Dear all,
> I would like to know if there is any method where I can calculate all
> the relative maximums in a 3D image and then, with these points
> (relative maximums) create a new image.
>
> Thanks for your help
> Best regards
> Irene
>
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users
>
------------------------------
Message: 4
Date: Tue, 27 May 2008 20:04:48 +0200
From: Ga?tan Lehmann <gaetan.lehmann at jouy.inra.fr>
Subject: Re: [Insight-users] Relative maximums
To: ITK Users <insight-users at itk.org>
Message-ID: <4E0D17A7-2E4A-46B5-8B19-F17D5D67781B at jouy.inra.fr>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
Hi,
Maybe also this one:
http://www.itk.org/Doxygen/html/classitk_1_1RegionalMaximaImageFilter.ht
ml
It will also work with floating pixel types.
Regards,
Ga?tan
Le 27 mai 08 ? 19:08, Xabier Artaechevarria Artieda a ?crit :
> Hi Irene,
> This filter might do what you are looking for:
>
> http://www.itk.org/Doxygen34/html/classitk_1_1HConvexImageFilter.html
>
> Best regards,
> Xabi
>
> --
> Xabier Artaechevarria
> Cancer Imaging Laboratory
> Centre for Applied Medical Research
> www.cima.es
>
>
>
> Irene Gonz?lvez Garc?a <irenegonzalvezg at gmail.com> ha escrito:
>
>> Dear all,
>> I would like to know if there is any method where I can calculate all
>> the relative maximums in a 3D image and then, with these points
>> (relative maximums) create a new image.
>>
>> Thanks for your help
>> Best regards
>> Irene
>>
>> _______________________________________________
>> Insight-users mailing list
>> Insight-users at itk.org
>> http://www.itk.org/mailman/listinfo/insight-users
>
>
>
> ----------------------------------------------------------------
> Este mensaje ha sido enviado desde https://webmail.unav.es
>
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users
--
Ga?tan Lehmann
Biologie du D?veloppement 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 http://www.mandriva.org
http://www.itk.org http://www.clavier-dvorak.org
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Message: 5
Date: Tue, 27 May 2008 20:09:14 +0200
From: Ga?tan Lehmann <gaetan.lehmann at jouy.inra.fr>
Subject: Re: [Insight-users] Wrap IKT repeats wrapping during make
install?
To: Dan White <white at mpi-cbg.de>
Cc: ITK <insight-users at itk.org>
Message-ID: <16091E97-4AC2-4074-B2B9-A4B690EA1915 at jouy.inra.fr>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed";
DelSp="yes"
Hi Dan,
Le 27 mai 08 ? 13:29, Dan White a ?crit :
> Dear Gaetan,
>
> I'm doing the ITK CVS build/install now (in source tree build)
> and that went very well, no errors.
>
> but now i am doing
> make install
> (installing into my system python on OSX 10.5)
> and the whole python wrapping process seems to be repeated....
> which takes a very long time....
>
> is this supposed to happen both for
> make
> and for
> make install
No, it's not supposed to be repeated.
I'm not able to reproduce that on my side, so I can't tell you more.
Brad gave me a cmake option a long time ago, to disable the build
during "make install". I can't find it though, but I know it exists :P
Regards,
Ga?tan
--
Ga?tan Lehmann
Biologie du D?veloppement 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 http://www.mandriva.org
http://www.itk.org http://www.clavier-dvorak.org
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Message: 6
Date: Tue, 27 May 2008 16:41:00 -0500
From: "Blezek, Daniel J., Ph.D." <Blezek.Daniel at mayo.edu>
Subject: [Insight-users] Dice Similarity Coefficient in ITK?
To: <insight-users at itk.org>, <insight-developers at itk.org>
Message-ID:
<E4316D745DA3094EA00191F6C205638B01029F24 at msgebe14.mfad.mfroot.org>
Content-Type: text/plain; charset="us-ascii"
Hi all,
I'm looking to collect a few overlap measures, e.g. Hausdorff, Dice in
ITK, but didn't want to reimplement if could be avoided. I found the
Hausdorff filter, but "no Dice". 8)
Any pointers would be greatly appreciated,
-dan
Daniel Blezek, PhD
Medical Imaging Informatics Innovation Center
Enterprise Imaging Systems Unit
P 127 or (77) 8 8886
T 507 538 8886
E blezek.daniel at mayo.edu
Mayo Clinic
200 First St. S.W.
Harwick SL-44
Rochester, MN 55905
mayoclinic.org
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Message: 7
Date: Tue, 27 May 2008 21:57:52 +0000
From: "Karthik Krishnan" <karthik.krishnan at kitware.com>
Subject: Re: [Insight-users] [Insight-developers] Dice Similarity
Coefficient in ITK?
To: "Blezek, Daniel J., Ph.D." <Blezek.Daniel at mayo.edu>
Cc: insight-users at itk.org, insight-developers at itk.org
Message-ID:
<9ddb27260805271457m7badd29by1b218bb1a4ff02e1 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
On Tue, May 27, 2008 at 9:41 PM, Blezek, Daniel J., Ph.D.
<Blezek.Daniel at mayo.edu> wrote:
> Hi all,
>
> I'm looking to collect a few overlap measures, e.g. Hausdorff, Dice
in
> ITK, but didn't want to reimplement if could be avoided. I found the
> Hausdorff filter, but "no Dice". 8)
It goes by the more obscure name
itk::SimilarityIndexImageFilter
:)
------------------------------
Message: 8
Date: Wed, 28 May 2008 01:51:17 +0200
From: andreasfm at web.de
Subject: [Insight-users] Cannot change the series description
(0008|103E) of a dicom file using ITK
To: insight-users at itk.org
Message-ID: <1087187743 at web.de>
Content-Type: text/plain; charset=iso-8859-15
Dear ITK users!
I want to change the header of a dicom file. It works fine with all but
one dicom tag. I cannot change the series description (0008|103E).
My code below is adapted from DicomImageReadChangeHeaderWrite.
Does anyone know why
itk::EncapsulateMetaData<string>( dictionary, "0008|103E", "a new
series description, THIS DOES NOT WORK" );
is not working, i.e. after saving the dicom file the tags has not
changed?
Thanks,
Andreas
//****
typedef itk::ImageFileReader<TImage> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(inputFile);
typedef itk::GDCMImageIO ImageIOType;
ImageIOType::Pointer gdcmImageIO = ImageIOType::New();
reader->SetImageIO( gdcmImageIO );
TImage::Pointer inputImage = reader->GetOutput();
typedef itk::MetaDataDictionary DictionaryType;
DictionaryType& dictionary = inputImage->GetMetaDataDictionary();
itk::EncapsulateMetaData<string>( dictionary, "0008|1010", "a new
station name, THIS WORKS" );
itk::EncapsulateMetaData<string>( dictionary, "0008|103E", "a new series
description, THIS DOES NOT WORK" );
typedef itk::ImageFileWriter<TImageSShort2D> WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetInput(reader->GetOutput());
writer->SetFileName(outputFile);
writer->SetImageIO(gdcmImageIO);
writer->Update();
------------------------------
Message: 9
Date: Tue, 27 May 2008 20:19:49 -0400
From: Bill Hoffman <bill.hoffman at kitware.com>
Subject: Re: [Insight-users] [Insight-developers] ITK factory, MacOSX,
.so, .dylib
To: Sebastien BARRE <sebastien.barre at kitware.com>
Cc: insight-users at itk.org, insight-developers at itk.org, Steve Pieper
<pieper at bwh.harvard.edu>
Message-ID: <483CA525.7060108 at kitware.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Sebastien BARRE wrote:
> Hello ITK,
>
> Quick question: was the factory mechanism on MacOSX fixed so that ITK
> looks for .dylib instead of .so.
>
> I see a few hacks in Slicer3 (which uses ITK 2.6) where IO plugin
> libraries are built (i.e. as .dylib), then a POST_BUILD custom command
> is added to copy it to the same library name, but with a .so
extension,
> so that ITK can load it at run-time. And then I realized the .so libs
> are not even installed, so that's not helping :) Anyway, instead of
> fixing the install rule for the .so, can you guys tell me if I can get
> rid of the POST_BUILD command altogether and expect ITK 2.6 to load
> .dylib fine?
>
On older versions of MACOSX you could not load a .dylib. This is a
recent addition to MacOSX. The .so is a loadable module on the Mac.
So, I don't think you can get rid of it.
-Bill
------------------------------
Message: 10
Date: Tue, 27 May 2008 21:55:24 -0400
From: "Bill Lorensen" <bill.lorensen at gmail.com>
Subject: Re: [Insight-users] [Insight-developers] ITK factory, MacOSX,
.so, .dylib
To: "Sebastien BARRE" <sebastien.barre at kitware.com>
Cc: insight-users at itk.org, insight-developers at itk.org, Steve Pieper
<pieper at bwh.harvard.edu>
Message-ID:
<4db4735c0805271855t78ebfccj731b240567509f55 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
I believe that in Slicer3/Libs/ModuleDescription/ModuleFactory.cxx we
use itksys::DynamicLoader::LibExtension() except for the MAC, where we
return ".dylib" as the extension. We did this because kwsys changed
the way it returned the extenstion for MAC. We also did the same for
Insight/Code/Common/itkObjectFactoryBase.cxx.
Bill
On Tue, May 27, 2008 at 7:53 PM, Sebastien BARRE
<sebastien.barre at kitware.com> wrote:
> Hello ITK,
>
> Quick question: was the factory mechanism on MacOSX fixed so that ITK
looks
> for .dylib instead of .so.
>
> I see a few hacks in Slicer3 (which uses ITK 2.6) where IO plugin
libraries
> are built (i.e. as .dylib), then a POST_BUILD custom command is added
to
> copy it to the same library name, but with a .so extension, so that
ITK can
> load it at run-time. And then I realized the .so libs are not even
> installed, so that's not helping :) Anyway, instead of fixing the
install
> rule for the .so, can you guys tell me if I can get rid of the
POST_BUILD
> command altogether and expect ITK 2.6 to load .dylib fine?
>
> Thanks
>
> _______________________________________________
> Insight-developers mailing list
> Insight-developers at itk.org
> http://www.itk.org/mailman/listinfo/insight-developers
>
------------------------------
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