From gregthom992 at gmail.com Sat Feb 3 01:39:33 2018 From: gregthom992 at gmail.com (G Tom) Date: Sat, 3 Feb 2018 01:39:33 -0500 Subject: [ITK-users] Extract Line/Intensity profile from image given start and stop points In-Reply-To: References: <1517433832235-0.post@n7.nabble.com> Message-ID: Do you have an idea how to do this averaging over the line with a radius ? I am also looking at vtkprobefilter. Thanks GT On Wed, Jan 31, 2018 at 6:01 PM, D?enan Zuki? wrote: > Hi Tom, > > BresenhamLine does not have a radius, it is only one pixel wide. If you > need some kind of averaging, you will probably need to resample the image. > There was a similar question last year, that thread > > will probably be helpful. > > Regards, > D?enan > > On Wed, Jan 31, 2018 at 4:23 PM, gregthom992 > wrote: > >> Hi Dzenan, >> >> itk::BresenhamLine seems to be what I need. Thanks for pointing that out. >> I >> am going through the example, how do I give it a radius ? >> >> Thanks >> >> GT >> >> >> >> -- >> Sent from: http://itk-users.7.n7.nabble.com/ >> The ITK community is transitioning from this mailing list to >> discourse.itk.org. Please join us there! >> ________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> https://itk.org/mailman/listinfo/insight-users >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregthom992 at gmail.com Sat Feb 3 02:37:40 2018 From: gregthom992 at gmail.com (G Tom) Date: Sat, 3 Feb 2018 02:37:40 -0500 Subject: [ITK-users] Extract Line/Intensity profile from image given start and stop points In-Reply-To: References: <1517433832235-0.post@n7.nabble.com>

Message-ID: Hi , I looked at the link you mentioned; the idea that comes to mind now is that I first rotate my image so that one of the axis is aligned with the line, then extract scan line along the rotated image axis possibly after re sampling. How do I rotate the image about a line defined by two points ? On Sat, Feb 3, 2018 at 1:39 AM, G Tom wrote: > Do you have an idea how to do this averaging over the line with a radius ? > > I am also looking at vtkprobefilter. > > Thanks > > GT > > On Wed, Jan 31, 2018 at 6:01 PM, D?enan Zuki? wrote: > >> Hi Tom, >> >> BresenhamLine does not have a radius, it is only one pixel wide. If you >> need some kind of averaging, you will probably need to resample the image. >> There was a similar question last year, that thread >> >> will probably be helpful. >> >> Regards, >> D?enan >> >> On Wed, Jan 31, 2018 at 4:23 PM, gregthom992 >> wrote: >> >>> Hi Dzenan, >>> >>> itk::BresenhamLine seems to be what I need. Thanks for pointing that >>> out. I >>> am going through the example, how do I give it a radius ? >>> >>> Thanks >>> >>> GT >>> >>> >>> >>> -- >>> Sent from: http://itk-users.7.n7.nabble.com/ >>> The ITK community is transitioning from this mailing list to >>> discourse.itk.org. Please join us there! >>> ________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> https://itk.org/mailman/listinfo/insight-users >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Mon Feb 5 11:20:18 2018 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 5 Feb 2018 11:20:18 -0500 Subject: [ITK-users] Extract Line/Intensity profile from image given start and stop points In-Reply-To: References: <1517433832235-0.post@n7.nabble.com>

Message-ID: Hi, resample image filter can do the heavy lifting. But you do need to provide an appropriate transform , relying on linear algebra - point transformations etc. Regards, D?enan On Sat, Feb 3, 2018 at 2:37 AM, G Tom wrote: > Hi , > I looked at the link you mentioned; the idea that comes to mind now is > that I first rotate my image so that one of the axis is aligned with the > line, then extract scan line along the rotated image axis possibly after re > sampling. > How do I rotate the image about a line defined by two points ? > > On Sat, Feb 3, 2018 at 1:39 AM, G Tom wrote: > >> Do you have an idea how to do this averaging over the line with a radius ? >> >> I am also looking at vtkprobefilter. >> >> Thanks >> >> GT >> >> On Wed, Jan 31, 2018 at 6:01 PM, D?enan Zuki? wrote: >> >>> Hi Tom, >>> >>> BresenhamLine does not have a radius, it is only one pixel wide. If you >>> need some kind of averaging, you will probably need to resample the image. >>> There was a similar question last year, that thread >>> >>> will probably be helpful. >>> >>> Regards, >>> D?enan >>> >>> On Wed, Jan 31, 2018 at 4:23 PM, gregthom992 >>> wrote: >>> >>>> Hi Dzenan, >>>> >>>> itk::BresenhamLine seems to be what I need. Thanks for pointing that >>>> out. I >>>> am going through the example, how do I give it a radius ? >>>> >>>> Thanks >>>> >>>> GT >>>> >>>> >>>> >>>> -- >>>> Sent from: http://itk-users.7.n7.nabble.com/ >>>> The ITK community is transitioning from this mailing list to >>>> discourse.itk.org. Please join us there! >>>> ________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> https://itk.org/mailman/listinfo/insight-users >>>> >>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Tue Feb 6 02:39:03 2018 From: julien.jomier at kitware.com (Julien Jomier) Date: Tue, 6 Feb 2018 08:39:03 +0100 Subject: [ITK-users] [ANN] CMake Training Course in Singapore - March 27-28 In-Reply-To: <2d50072b-a62a-a58a-19a2-dd2747a38b39@kitware.com> References: <2d50072b-a62a-a58a-19a2-dd2747a38b39@kitware.com> Message-ID: <8f00f380-bba3-4436-c368-4d97dfb7cdb6@kitware.com> Kitware will be holding a CMake training course on March 27 and 28, 2018 in Singapore. This two-days course will cover the best practice for CMake, CTest, CPack and CDash as well as advanced features of the tool Please visit our website for more information and registration details: https://training.kitware.fr/browse/182 Note that the course will be taught in English. If you have any questions, please contact us at training at kitware.fr or email me directly. We are looking forward to seeing you in Singapore, Julien -- Kitware SAS 26 rue Louis Gu?rin 69100 Villeurbanne, France http://www.kitware.eu From ibr_ex at yahoo.com Thu Feb 8 05:36:44 2018 From: ibr_ex at yahoo.com (Ibraheem) Date: Thu, 8 Feb 2018 03:36:44 -0700 (MST) Subject: [ITK-users] ResampleDICOM example and DCMTK In-Reply-To: References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com> <1409515613801-7586158.post@n2.nabble.com>

Message-ID: <1518086204763-0.post@n7.nabble.com> Hi Matt, I have the same problem. I don't understand your answer. Part 3 of the code extract and create the meta data. The writer uses DCMTKImageIO as in : seriesWriter->SetImageIO(gdcmIO ); Could you please add more explaination! Best! Ibraheem -- Sent from: http://itk-users.7.n7.nabble.com/ From dzenanz at gmail.com Thu Feb 8 09:36:36 2018 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 8 Feb 2018 09:36:36 -0500 Subject: [ITK-users] ResampleDICOM example and DCMTK In-Reply-To: <1518086204763-0.post@n7.nabble.com> References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com> <1409515613801-7586158.post@n2.nabble.com>

<1518086204763-0.post@n7.nabble.com> Message-ID: Hi Ibraheem, we are moving away from a mailing list, and into a forum . Could you repost your question there? Thanks, D?enan On Thu, Feb 8, 2018 at 5:36 AM, Ibraheem via Insight-users < insight-users at itk.org> wrote: > Hi Matt, > I have the same problem. I don't understand your answer. Part 3 of the code > extract and create the meta data. The writer uses DCMTKImageIO as in : > seriesWriter->SetImageIO(gdcmIO ); > > Could you please add more explaination! > Best! > Ibraheem > > > > > -- > Sent from: http://itk-users.7.n7.nabble.com/ > The ITK community is transitioning from this mailing list to > discourse.itk.org. Please join us there! > ________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > https://itk.org/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ibr_ex at yahoo.com Thu Feb 8 09:48:29 2018 From: ibr_ex at yahoo.com (ibraheem aldhamari) Date: Thu, 8 Feb 2018 14:48:29 +0000 (UTC) Subject: [ITK-users] ResampleDICOM example and DCMTK In-Reply-To: References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com> <1409515613801-7586158.post@n2.nabble.com>

<1518086204763-0.post@n7.nabble.com> Message-ID: <1916463187.372506.1518101309421@mail.yahoo.com> Thanks, this is a great news!I will do so.?Best! On Thursday, February 8, 2018, 3:36:59 PM GMT+1, D?enan Zuki? wrote: Hi Ibraheem, we are moving away from a mailing list, and into a forum. Could you repost your question there? Thanks,D?enan On Thu, Feb 8, 2018 at 5:36 AM, Ibraheem via Insight-users wrote: Hi Matt, I have the same problem. I don't understand your answer. Part 3 of the code extract and create the meta data. The writer uses DCMTKImageIO as in : seriesWriter->SetImageIO( gdcmIO ); Could you please add more explaination! Best! Ibraheem -- Sent from: http://itk-users.7.n7.nabble. com/ The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there! ______________________________ __ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/ opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/ products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_ FAQ Follow this link to subscribe/unsubscribe: https://itk.org/mailman/ listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From dclunie at dclunie.com Thu Feb 8 10:11:46 2018 From: dclunie at dclunie.com (David Clunie) Date: Thu, 8 Feb 2018 10:11:46 -0500 Subject: [ITK-users] Forums suck, long live email, was Re: ResampleDICOM example and DCMTK In-Reply-To: References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com> <1409515613801-7586158.post@n2.nabble.com>

<1518086204763-0.post@n7.nabble.com> Message-ID: <86a1fc0e-2c66-0e5c-5941-c348f99658f0@dclunie.com> That's a bummer ... now I won't be able to have all the mail to the list archived and indexed in a standard format along with all the other lists that I subscribe to, so that I can search everything at once, and instead it will be hidden on some inaccessible proprietary system with dubious longevity. Is there a way to have discourse.itk.org forward every message by email? I couldn't find one. David On 2/8/18 9:36 AM, D?enan Zuki? wrote: > Hi Ibraheem, > > we are moving away from a mailing list, and into a forum . Could you repost your question there? > > Thanks, > D?enan From dzenanz at gmail.com Thu Feb 8 10:46:31 2018 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 8 Feb 2018 10:46:31 -0500 Subject: [ITK-users] Forums suck, long live email, was Re: ResampleDICOM example and DCMTK In-Reply-To: <86a1fc0e-2c66-0e5c-5941-c348f99658f0@dclunie.com> References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com> <1409515613801-7586158.post@n2.nabble.com>

<1518086204763-0.post@n7.nabble.com> <86a1fc0e-2c66-0e5c-5941-c348f99658f0@dclunie.com> Message-ID: Yes, there is. For me, the "mailing list mode" is found on this page: https://discourse.itk.org/u/dzenanz/preferences/emails Regards, D?enan On Thu, Feb 8, 2018 at 10:11 AM, David Clunie wrote: > That's a bummer ... now I won't be able to have all the mail > to the list archived and indexed in a standard format along > with all the other lists that I subscribe to, so that I can > search everything at once, and instead it will be hidden on > some inaccessible proprietary system with dubious longevity. > > Is there a way to have discourse.itk.org forward every message > by email? I couldn't find one. > > David > > On 2/8/18 9:36 AM, D?enan Zuki? wrote: > > Hi Ibraheem, > > > > we are moving away from a mailing list, and into a forum < > https://discourse.itk.org/>. Could you repost your question there? > > > > Thanks, > > D?enan > The ITK community is transitioning from this mailing list to > discourse.itk.org. Please join us there! > ________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > https://itk.org/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Thu Feb 8 10:47:55 2018 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 8 Feb 2018 10:47:55 -0500 Subject: [ITK-users] Forums suck, long live email, was Re: ResampleDICOM example and DCMTK In-Reply-To: <86a1fc0e-2c66-0e5c-5941-c348f99658f0@dclunie.com> References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com> <1409515613801-7586158.post@n2.nabble.com>

<1518086204763-0.post@n7.nabble.com> <86a1fc0e-2c66-0e5c-5941-c348f99658f0@dclunie.com> Message-ID: Hi David, Thanks for chiming in. Don't worry, email lives on :-). Instructions on how to use Discourse as a mailing list can be found here: https://discourse.itk.org/t/using-discourse-as-a-mailing-list/32 Thanks, Matt On Thu, Feb 8, 2018 at 10:11 AM, David Clunie wrote: > That's a bummer ... now I won't be able to have all the mail > to the list archived and indexed in a standard format along > with all the other lists that I subscribe to, so that I can > search everything at once, and instead it will be hidden on > some inaccessible proprietary system with dubious longevity. > > Is there a way to have discourse.itk.org forward every message > by email? I couldn't find one. > > David > > On 2/8/18 9:36 AM, D?enan Zuki? wrote: >> Hi Ibraheem, >> >> we are moving away from a mailing list, and into a forum . Could you repost your question there? >> >> Thanks, >> D?enan > The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there! > ________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > https://itk.org/mailman/listinfo/insight-users From bill.lorensen at gmail.com Thu Feb 8 11:46:31 2018 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Thu, 8 Feb 2018 08:46:31 -0800 Subject: [ITK-users] Forums suck, long live email, was Re: ResampleDICOM example and DCMTK In-Reply-To: References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com> <1409515613801-7586158.post@n2.nabble.com>

<1518086204763-0.post@n7.nabble.com> <86a1fc0e-2c66-0e5c-5941-c348f99658f0@dclunie.com> Message-ID: David, I agree. I only use the email option for discourse. On Feb 8, 2018 7:48 AM, "Matt McCormick" wrote: > Hi David, > > Thanks for chiming in. Don't worry, email lives on :-). > > Instructions on how to use Discourse as a mailing list can be found here: > > https://discourse.itk.org/t/using-discourse-as-a-mailing-list/32 > > Thanks, > Matt > > On Thu, Feb 8, 2018 at 10:11 AM, David Clunie wrote: > > That's a bummer ... now I won't be able to have all the mail > > to the list archived and indexed in a standard format along > > with all the other lists that I subscribe to, so that I can > > search everything at once, and instead it will be hidden on > > some inaccessible proprietary system with dubious longevity. > > > > Is there a way to have discourse.itk.org forward every message > > by email? I couldn't find one. > > > > David > > > > On 2/8/18 9:36 AM, D?enan Zuki? wrote: > >> Hi Ibraheem, > >> > >> we are moving away from a mailing list, and into a forum < > https://discourse.itk.org/>. Could you repost your question there? > >> > >> Thanks, > >> D?enan > > The ITK community is transitioning from this mailing list to > discourse.itk.org. Please join us there! > > ________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > https://itk.org/mailman/listinfo/insight-users > The ITK community is transitioning from this mailing list to > discourse.itk.org. Please join us there! > ________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > https://itk.org/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From majid.msadeghi at yahoo.com Mon Feb 12 06:41:40 2018 From: majid.msadeghi at yahoo.com (Majid M. Sadeghi) Date: Mon, 12 Feb 2018 11:41:40 +0000 (UTC) Subject: [ITK-users] ITK Noise removal filter on VTK file References: <1745079269.3165284.1518435700616.ref@mail.yahoo.com> Message-ID: <1745079269.3165284.1518435700616@mail.yahoo.com> Dear All, I am using a vtkGDCMImageReader to import 3D DICOM images. Then I adjust the spacing and reslice. After that I can save it as both image data|(vtkXMLImageDataWriter) or polydata(vtkImageDataGeometryFilter). I want to apply edge preserving noise removal to the data either just after reading images, or after saving as .vtp files. I have setup ITK and scanned the ITK book, but I have no experience on it. Is there any link or example which can guide me on how to perform this? (what type of structure is common between ITK and VTK? Should I perform the filter after saving in VTK or before that? which filter do you suggest for the best speed and perfomance?) Thanks a lot. -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Feb 12 07:27:32 2018 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 12 Feb 2018 07:27:32 -0500 Subject: [ITK-users] ITK Noise removal filter on VTK file In-Reply-To: <1745079269.3165284.1518435700616@mail.yahoo.com> References: <1745079269.3165284.1518435700616.ref@mail.yahoo.com> <1745079269.3165284.1518435700616@mail.yahoo.com> Message-ID: Hi Majid, For the best DICOM image compatibility, use itk::DCMTKImageIO: https://github.com/InsightSoftwareConsortium/ITK/blob/8a2a15f41218c925c0a89119e09419d48f83eb22/Modules/IO/DCMTK/test/itkDCMTKSeriesReadImageWrite.cxx This also supports reading in the DICOM image orientation into the itk::Image. This information is not retained in vtkImageData. Writing the image to disk can be avoided with ITKVtkGlue: https://itk.org/ITKExamples/src/Bridge/VtkGlue/ConvertAnitkImageTovtkImageData/Documentation.html but again, be aware of the loss of the Direction information. Both ITK and VTK support image volumes written in MetaImage, NRRD, or VTK Legacy file format. A state-of-the-art edge preserving filter is the anisotropic diffusion lattice basis reduction filter in ITK. For more information, see the Insight Journal article: http://www.insight-journal.org/browse/publication/953 and instructions on how to install the Python package or enable its module in ITK's build here: https://github.com/InsightSoftwareConsortium/ITKAnisotropicDiffusionLBR Hope this helps, Matt On Mon, Feb 12, 2018 at 6:41 AM, Majid M. Sadeghi via Insight-users wrote: > Dear All, > > I am using a vtkGDCMImageReader to import 3D DICOM images. Then I adjust the > spacing and reslice. After that I can save it as both image > data|(vtkXMLImageDataWriter) or polydata(vtkImageDataGeometryFilter). > > I want to apply edge preserving noise removal to the data either just after > reading images, or after saving as .vtp files. > > I have setup ITK and scanned the ITK book, but I have no experience on it. > > Is there any link or example which can guide me on how to perform this? > (what type of structure is common between ITK and VTK? Should I perform the > filter after saving in VTK or before that? which filter do you suggest for > the best speed and perfomance?) > > Thanks a lot. > > > The ITK community is transitioning from this mailing list to > discourse.itk.org. Please join us there! > ________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > https://itk.org/mailman/listinfo/insight-users > From majid.msadeghi at yahoo.com Mon Feb 12 07:58:29 2018 From: majid.msadeghi at yahoo.com (Majid M. Sadeghi) Date: Mon, 12 Feb 2018 12:58:29 +0000 (UTC) Subject: [ITK-users] ITK Noise removal filter on VTK file In-Reply-To: References: <1745079269.3165284.1518435700616.ref@mail.yahoo.com> <1745079269.3165284.1518435700616@mail.yahoo.com> Message-ID: <728315313.3213510.1518440309490@mail.yahoo.com> Thank you so much for the great help. On Monday, February 12, 2018 2:27 PM, Matt McCormick wrote: Hi Majid, For the best DICOM image compatibility, use itk::DCMTKImageIO: ? https://github.com/InsightSoftwareConsortium/ITK/blob/8a2a15f41218c925c0a89119e09419d48f83eb22/Modules/IO/DCMTK/test/itkDCMTKSeriesReadImageWrite.cxx This also supports reading in the DICOM image orientation into the itk::Image. This information is not retained in vtkImageData. Writing the image to disk can be avoided with ITKVtkGlue: ? https://itk.org/ITKExamples/src/Bridge/VtkGlue/ConvertAnitkImageTovtkImageData/Documentation.html but again, be aware of the loss of the Direction information. Both ITK and VTK support image volumes written in MetaImage, NRRD, or VTK Legacy file format. A state-of-the-art edge preserving filter is the anisotropic diffusion lattice basis reduction filter in ITK. For more information, see the Insight Journal article: ? http://www.insight-journal.org/browse/publication/953 and instructions on how to install the Python package or enable its module in ITK's build here: ? https://github.com/InsightSoftwareConsortium/ITKAnisotropicDiffusionLBR Hope this helps, Matt On Mon, Feb 12, 2018 at 6:41 AM, Majid M. Sadeghi via Insight-users wrote: > Dear All, > > I am using a vtkGDCMImageReader to import 3D DICOM images. Then I adjust the > spacing and reslice. After that I can save it as both image > data|(vtkXMLImageDataWriter) or polydata(vtkImageDataGeometryFilter). > > I want to apply edge preserving noise removal to the data either just after > reading images, or after saving as .vtp files. > > I have setup ITK and scanned the ITK book, but I have no experience on it. > > Is there any link or example which can guide me on how to perform this? > (what type of structure is common between ITK and VTK? Should I perform the > filter after saving in VTK or before that? which filter do you suggest for > the best speed and perfomance?) > > Thanks a lot. > > > The ITK community is transitioning from this mailing list to > discourse.itk.org. Please join us there! > ________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > https://itk.org/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From majid.msadeghi at yahoo.com Tue Feb 13 11:31:57 2018 From: majid.msadeghi at yahoo.com (Majid M. Sadeghi) Date: Tue, 13 Feb 2018 16:31:57 +0000 (UTC) Subject: [ITK-users] Convert vtkImageData to an itk::Image References: <271213644.174330.1518539517781.ref@mail.yahoo.com> Message-ID: <271213644.174330.1518539517781@mail.yahoo.com> Dear All, I read some DICOM data using vtkGDCMImageReader, then I change the sapacing and reslice them. Next I want to change that vtk image to itk image to be able to apply noise removal. But as soon as the code reaches the "filter_toitkimage->Update();" line the program just exits without saying anything (actually it says:The program '[14040] QtGuiApplication2.exe' has exited with code 3 (0x3).). Here is the code: vtkSmartPointer reader = vtkSmartPointer::New(); ??? reader->SetFileNames(vtkfiles); ??? reader->Update(); ??? ??? vtkSmartPointer changer = vtkSmartPointer::New(); ??? changer->SetOutputSpacing(pixlespacing, pixlespacing, ippzspacing);//@majidnow ??? changer->SetInputConnection(reader->GetOutputPort()); ??? vtkSmartPointer reslice = vtkSmartPointer::New(); ??? reslice->SetInputConnection(changer->GetOutputPort()); ??? ??? //to change VTK image to ITK image ??? const unsigned int Dimension = 3; ??? using PixelType = double; ??? using ImageType = itk::Image< PixelType, Dimension >; ??? using FilterType = itk::VTKImageToImageFilter< ImageType >; ??? FilterType::Pointer filter_toitkimage = FilterType::New(); ??? filter_toitkimage->SetInput(reslice->GetOutput()); ??? try ??? { ??? ??? filter_toitkimage->Update(); ??? } ??? catch (itk::ExceptionObject & error) ??? { ??? ??? std::cerr << "Error: " << error << std::endl; ??? ??? //return EXIT_FAILURE; ??? }? Any idea why this happens? -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Tue Feb 13 15:16:43 2018 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 13 Feb 2018 15:16:43 -0500 Subject: [ITK-users] [vtkusers] Convert vtkImageData to an itk::Image In-Reply-To: <271213644.174330.1518539517781@mail.yahoo.com> References: <271213644.174330.1518539517781.ref@mail.yahoo.com> <271213644.174330.1518539517781@mail.yahoo.com> Message-ID: Hi Majid, maybe you need to invoke reslice->Update(); before importing its output into ITK? Regards, D?enan On Tue, Feb 13, 2018 at 11:31 AM, Majid M. Sadeghi via vtkusers < vtkusers at vtk.org> wrote: > Dear All, > > I read some DICOM data using vtkGDCMImageReader, then I change the > sapacing and reslice them. Next I want to change that vtk image to itk > image to be able to apply noise removal. But as soon as the code reaches > the "filter_toitkimage->Update();" line the program just exits without > saying anything (actually it says:The program '[14040] > QtGuiApplication2.exe' has exited with code 3 (0x3).). > > Here is the code: > > vtkSmartPointer reader = vtkSmartPointer< > vtkGDCMImageReader>::New(); > reader->SetFileNames(vtkfiles); > reader->Update(); > > vtkSmartPointer changer = vtkSmartPointer< > vtkImageChangeInformation>::New(); > changer->SetOutputSpacing(pixlespacing, pixlespacing, > ippzspacing);//@majidnow > changer->SetInputConnection(reader->GetOutputPort()); > > vtkSmartPointer reslice = vtkSmartPointer< > vtkImageReslice>::New(); > reslice->SetInputConnection(changer->GetOutputPort()); > > //to change VTK image to ITK image > const unsigned int Dimension = 3; > > using PixelType = double; > using ImageType = itk::Image< PixelType, Dimension >; > > using FilterType = itk::VTKImageToImageFilter< ImageType >; > FilterType::Pointer filter_toitkimage = FilterType::New(); > filter_toitkimage->SetInput(reslice->GetOutput()); > > try > { > filter_toitkimage->Update(); > } > catch (itk::ExceptionObject & error) > { > std::cerr << "Error: " << error << std::endl; > //return EXIT_FAILURE; > } > > > Any idea why this happens? > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at http://www.kitware.com/ > opensource/opensource.html > > Please keep messages on-topic and check the VTK FAQ at: > http://www.vtk.org/Wiki/VTK_FAQ > > Search the list archives at: http://markmail.org/search/?q=vtkusers > > Follow this link to subscribe/unsubscribe: > https://vtk.org/mailman/listinfo/vtkusers > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Wed Feb 14 02:32:57 2018 From: julien.jomier at kitware.com (Julien Jomier) Date: Wed, 14 Feb 2018 08:32:57 +0100 Subject: [ITK-users] [ANN] CMake Training Course in France - March 12 Message-ID: Kitware will be holding a CMake training course on March 12, 2018 in Lyon, France. This one-day course will cover the best practice for CMake, CTest, CPack and CDash. Please visit our website for more information and registration details: https://training.kitware.fr/browse/170 Note that the course will be taught in English. If you have any questions, please contact us at training at kitware.fr or email me directly. We are looking forward to seeing you in Lyon, Julien -- Kitware SAS 26 rue Louis Gu?rin 69100 Villeurbanne, France http://www.kitware.eu From majid.msadeghi at yahoo.com Wed Feb 14 04:05:20 2018 From: majid.msadeghi at yahoo.com (Majid M. Sadeghi) Date: Wed, 14 Feb 2018 09:05:20 +0000 (UTC) Subject: [ITK-users] [vtkusers] Convert vtkImageData to an itk::Image In-Reply-To: References: <271213644.174330.1518539517781.ref@mail.yahoo.com> <271213644.174330.1518539517781@mail.yahoo.com> Message-ID: <424306771.685882.1518599120779@mail.yahoo.com> Thanks, that did the job, sometimes silly mistakes create a headache. ? On Tuesday, February 13, 2018 10:17 PM, D?enan Zuki? wrote: Hi Majid, maybe you need to invoke?reslice->Update(); before importing its output into ITK? Regards,D?enan On Tue, Feb 13, 2018 at 11:31 AM, Majid M. Sadeghi via vtkusers wrote: Dear All, I read some DICOM data using vtkGDCMImageReader, then I change the sapacing and reslice them. Next I want to change that vtk image to itk image to be able to apply noise removal. But as soon as the code reaches the "filter_toitkimage->Update();" line the program just exits without saying anything (actually it says:The program '[14040] QtGuiApplication2.exe' has exited with code 3 (0x3).). Here is the code: vtkSmartPointer< vtkGDCMImageReader> reader = vtkSmartPointer< vtkGDCMImageReader>::New(); ??? reader->SetFileNames(vtkfiles) ; ??? reader->Update(); ??? ??? vtkSmartPointer< vtkImageChangeInformation> changer = vtkSmartPointer< vtkImageChangeInformation>:: New(); ??? changer->SetOutputSpacing( pixlespacing, pixlespacing, ippzspacing);//@majidnow ??? changer->SetInputConnection( reader->GetOutputPort()); ??? vtkSmartPointer< vtkImageReslice> reslice = vtkSmartPointer< vtkImageReslice>::New(); ??? reslice->SetInputConnection( changer->GetOutputPort()); ??? ??? //to change VTK image to ITK image ??? const unsigned int Dimension = 3; ??? using PixelType = double; ??? using ImageType = itk::Image< PixelType, Dimension >; ??? using FilterType = itk::VTKImageToImageFilter< ImageType >; ??? FilterType::Pointer filter_toitkimage = FilterType::New(); ??? filter_toitkimage->SetInput( reslice->GetOutput()); ??? try ??? { ??? ??? filter_toitkimage->Update(); ??? } ??? catch (itk::ExceptionObject & error) ??? { ??? ??? std::cerr << "Error: " << error << std::endl; ??? ??? //return EXIT_FAILURE; ??? }? Any idea why this happens? ______________________________ _________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/ opensource/opensource.html Please keep messages on-topic and check the VTK FAQ at: http://www.vtk.org/Wiki/VTK_ FAQ Search the list archives at: http://markmail.org/search/?q= vtkusers Follow this link to subscribe/unsubscribe: https://vtk.org/mailman/ listinfo/vtkusers -------------- next part -------------- An HTML attachment was scrubbed... URL: From sean at rogue-research.com Wed Feb 14 17:14:01 2018 From: sean at rogue-research.com (Sean McBride) Date: Wed, 14 Feb 2018 17:14:01 -0500 Subject: [ITK-users] Forums suck, long live email, was Re: ResampleDICOM example and DCMTK In-Reply-To: References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com> <1409515613801-7586158.post@n2.nabble.com>

<1518086204763-0.post@n7.nabble.com> <86a1fc0e-2c66-0e5c-5941-c348f99658f0@dclunie.com> Message-ID: <20180214221401.1996920570@mail.rogue-research.com> On Thu, 8 Feb 2018 10:47:55 -0500, Matt McCormick said: >Thanks for chiming in. Don't worry, email lives on :-). > >Instructions on how to use Discourse as a mailing list can be found here: > > https://discourse.itk.org/t/using-discourse-as-a-mailing-list/32 Alas, in my opinion anyway, using Discourse as a mailing list is a very subpar experience. - it changes the 'from' address, making off-list replies impossible - replying to the 'from' address bounces, making 'reply all' broken - there's no 'List-Post' header, so it's hard to start new threads - it sends html email - the text-only part of the email renders quotations poorly - quoted text in replies get removed, making inline replies impossible/broken - it does something weird with emoji characters, changing them to strings like ":ok_hand:" - it discards email signatures Cheers, Sean From matt.mccormick at kitware.com Wed Feb 14 18:48:26 2018 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 14 Feb 2018 18:48:26 -0500 Subject: [ITK-users] [ITK] Forums suck, long live email, was Re: ResampleDICOM example and DCMTK In-Reply-To: References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com> <1409515613801-7586158.post@n2.nabble.com>

<1518086204763-0.post@n7.nabble.com> <86a1fc0e-2c66-0e5c-5941-c348f99658f0@dclunie.com> <20180214221401.1996920570@mail.rogue-research.com> Message-ID: On Wed, Feb 14, 2018 at 5:47 PM, Matthew Brett wrote: > On Wed, Feb 14, 2018 at 10:14 PM, Sean McBride wrote: >> On Thu, 8 Feb 2018 10:47:55 -0500, Matt McCormick said: >> >>>Thanks for chiming in. Don't worry, email lives on :-). >>> >>>Instructions on how to use Discourse as a mailing list can be found here: >>> >>> https://discourse.itk.org/t/using-discourse-as-a-mailing-list/32 >> >> Alas, in my opinion anyway, using Discourse as a mailing list is a very subpar experience. These statements are very deceiving. >> - it changes the 'from' address, making off-list replies impossible This means it does not expose your email address to all the spammers on the internets! >> - replying to the 'from' address bounces, making 'reply all' broken Use "reply" instead of "reply all". >> - there's no 'List-Post' header, so it's hard to start new threads See the link above on how to start a new thread. >> - it sends html email Yes, this is too bad. However, HTML email is simply a standard today in all kinds of communication. >> - the text-only part of the email renders quotations poorly I am not sure how bad this is relative having content only limited to plain text. In imaging, it is helpful to be able to share images. >> - quoted text in replies get removed, making inline replies impossible/broken It is still possible to quote replies. >> - it does something weird with emoji characters, changing them to strings like ":ok_hand:" Is this bad? >> - it discards email signatures This is a feature. 2 cents, Matt From bakkari.abdelkhalek at hotmail.fr Sat Feb 17 06:23:41 2018 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Sat, 17 Feb 2018 11:23:41 +0000 Subject: [ITK-users] Characterization degree using ITK Message-ID: Dear All, I am trying to compute the characterization degree for a statistical features of an image using ITK . This criterion is based on the report/ratio of the between classes (inter-class) variance by the intra-class variance, calculated in order to extract the best statistical features of an image. Could you please, provide me any help. Thank you in advance. Kind regards, -------------- next part -------------- An HTML attachment was scrubbed... URL: From mrguilfoyle at gmail.com Sat Feb 17 10:28:59 2018 From: mrguilfoyle at gmail.com (Mathew Guilfoyle) Date: Sat, 17 Feb 2018 15:28:59 +0000 Subject: [ITK-users] SimpleITK R Wrapping of ChangeLabel and ChangeMap Message-ID: <124D2356-CD65-4779-9BA5-56B2CB71682E@gmail.com> I am struggling to find the correct way to specify a ChangeMap to supply to the ChangeLabel filter in the R wrapping of SimpleITK. I can create the filter object but supplying a R list of (vector) pairs of from/to labels causes R to crash. Looking through the SimpleITK docs the ChangeMap is specified as a std::map structure and in the R SWIG file there is a DoubleDoubleMap() function specified which seems to be a mechanism to create the map in R. However, despite trying various ways of using the DoubleDoubleMap I cannot get it to work. I can create a DoubleDoubleMap object but then can't supplying the pairs of labels that define the map. One Python example I came across uses the DoubleDoubleMap like this: import SimpleITK as silk changeLabel = sitk.ChangeLabelImageFilter() changeMap = sitk.DoubleDoubleMap() changeMap[0] = 1 changeMap[1] = 2 etc.. Doing the equivalent indexing in R produces the error: Error: evaluation nested too deeply: infinite recursion / options(expressions=)? Error during wrapup: evaluation nested too deeply: infinite recursion / options(expressions=)? Does anyone know how to correctly interact with the DoubleDoubleMap object and/or otherwise specify a change map in R? Many thanks -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1380 bytes Desc: not available URL: From richard.beare at gmail.com Sat Feb 17 17:35:36 2018 From: richard.beare at gmail.com (Richard Beare) Date: Sun, 18 Feb 2018 09:35:36 +1100 Subject: [ITK-users] SimpleITK R Wrapping of ChangeLabel and ChangeMap In-Reply-To: <124D2356-CD65-4779-9BA5-56B2CB71682E@gmail.com> References: <124D2356-CD65-4779-9BA5-56B2CB71682E@gmail.com> Message-ID: I'm afraid this is one thing we haven't yet fixed up in the R bindings. There aren't useful generators of std::map class bindings in SWIG/R at present, so you just end up with the class pointers and no methods to construct or manipulate them. It's on my list. My original plan was to use named vectors for the common case changing labels, but there are certainly going to be messy issues in converting keys to strings. However this approach is probably most like the dictionary method used by python. On Sun, Feb 18, 2018 at 2:28 AM, Mathew Guilfoyle wrote: > I am struggling to find the correct way to specify a ChangeMap to supply > to the ChangeLabel filter in the R wrapping of SimpleITK. > > I can create the filter object but supplying a R list of (vector) pairs of > from/to labels causes R to crash. Looking through the SimpleITK docs the > ChangeMap is specified as a std::map structure and in the R > SWIG file there is a DoubleDoubleMap() function specified which seems to be > a mechanism to create the map in R. However, despite trying various ways > of using the DoubleDoubleMap I cannot get it to work. I can create a > DoubleDoubleMap object but then can't supplying the pairs of labels that > define the map. One Python example I came across uses the DoubleDoubleMap > like this: > > import SimpleITK as silk > > changeLabel = sitk.ChangeLabelImageFilter() > changeMap = sitk.DoubleDoubleMap() > > changeMap[0] = 1 > changeMap[1] = 2 > > etc.. > > Doing the equivalent indexing in R produces the error: > > Error: evaluation nested too deeply: infinite recursion / > options(expressions=)? > Error during wrapup: evaluation nested too deeply: infinite recursion / > options(expressions=)? > > Does anyone know how to correctly interact with the DoubleDoubleMap object > and/or otherwise specify a change map in R? > > Many thanks > > > The ITK community is transitioning from this mailing list to > discourse.itk.org. Please join us there! > ________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > https://itk.org/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Mon Feb 19 11:11:30 2018 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 19 Feb 2018 11:11:30 -0500 Subject: [ITK-users] Characterization degree using ITK In-Reply-To: References: Message-ID: Hi Abdelkhalek, your question is general and kind of vague. Giving example image and better describing the expected output would make it clearer. Also, posting to discourse would reach a more active audience. Regards, D?enan On Sat, Feb 17, 2018 at 6:23 AM, Abdelkhalek Bakkari < bakkari.abdelkhalek at hotmail.fr> wrote: > Dear All, > > > I am trying to compute the characterization degree for a statistical > features of an image using ITK . > > This criterion is based on the report/ratio of the between classes > (inter-class) variance by the intra-class variance, calculated in order to > extract the best statistical features of an image. > > > Could you please, provide me any help. > > > Thank you in advance. > > > > Kind regards, > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.lemaitre58 at gmail.com Sun Feb 25 10:26:11 2018 From: g.lemaitre58 at gmail.com (=?UTF-8?Q?Guillaume_Lema=C3=AEtre?=) Date: Sun, 25 Feb 2018 16:26:11 +0100 Subject: [ITK-users] VNL matrix with the Python wrapper Message-ID: Hi All, I am using the python wrapper of itk to manipulate. I checked the quick start guide ( http://itkpythonpackage.readthedocs.io/en/latest/Quick_start_guide.html#usage) to go from numpy to vnl matrices and vice-versa. However, I got into trouble when trying to use those utils with itk images. As a short example: ```python >>> import numpy as np >>> img = np.random.random((100, 100, 100)) >>> img_itk = itk.GetImageFromArray(img) >>> vnl_matrix = img_itk.GetDirection().GetVnlMatrix() >>> type(vnl_matrix) vnl_matrix_fixedPython.vnl_matrix_fixedD_3_3 >>> itk.GetArrayFromVnlMatrix(vnl_matrix) TypeError: in method 'itkPyVnlD__GetArrayViewFromVnlMatrix', argument 1 of type 'vnl_matrixD *' ``` So what would the proper way of converting this matrix into a numpy array or view. Cheers, -- Guillaume Lemaitre INRIA Saclay - Parietal team Center for Data Science Paris-Saclay https://glemaitre.github.io/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Mon Feb 26 09:33:07 2018 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 26 Feb 2018 09:33:07 -0500 Subject: [ITK-users] VNL matrix with the Python wrapper In-Reply-To: References: Message-ID: Hi Guillaume, we have switched to discourse forum for discussion. Can you repost your question there? Thanks, D?enan On Sun, Feb 25, 2018 at 10:26 AM, Guillaume Lema?tre wrote: > Hi All, > > I am using the python wrapper of itk to manipulate. I checked the quick > start guide (http://itkpythonpackage.readthedocs.io/en/latest/ > Quick_start_guide.html#usage) to go from numpy to vnl matrices and > vice-versa. However, I got into trouble when trying to use those utils with > itk images. As a short example: > > ```python > >>> import numpy as np > > >>> img = np.random.random((100, 100, 100)) > >>> img_itk = itk.GetImageFromArray(img) > > >>> vnl_matrix = img_itk.GetDirection().GetVnlMatrix() > >>> type(vnl_matrix) > vnl_matrix_fixedPython.vnl_matrix_fixedD_3_3 > > >>> itk.GetArrayFromVnlMatrix(vnl_matrix) > > TypeError: in method 'itkPyVnlD__GetArrayViewFromVnlMatrix', argument 1 > of type 'vnl_matrixD *' > ``` > > So what would the proper way of converting this matrix into a numpy array > or view. > > Cheers, > -- > Guillaume Lemaitre > INRIA Saclay - Parietal team > Center for Data Science Paris-Saclay > https://glemaitre.github.io/ > > The ITK community is transitioning from this mailing list to > discourse.itk.org. Please join us there! > ________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > https://itk.org/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: