From srbn.ghosh99 at gmail.com Mon Jun 3 18:52:35 2019 From: srbn.ghosh99 at gmail.com (Shrabani Ghosh) Date: Mon, 3 Jun 2019 15:52:35 -0700 (MST) Subject: [ITK] [ITK-users] Registration-- Mutual Information based for CT to CT 3D data Message-ID: <1559602355207-0.post@n2.nabble.com> I can see there are a lot of Registration programs in ITK. I want to do mutual information based registration for CT to CT 3D data . Please suggest me which one should I use. -- Sent from: http://itk-insight-users.2283740.n2.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 From srbn.ghosh99 at gmail.com Tue Jun 4 10:10:52 2019 From: srbn.ghosh99 at gmail.com (Shrabani Ghosh) Date: Tue, 4 Jun 2019 07:10:52 -0700 (MST) Subject: [ITK] [ITK-users] Registration-- Mutual Information based for CT to CT 3D data In-Reply-To: <631174203.307923.1559632166677@mail.yahoo.com> References: <1559602355207-0.post@n2.nabble.com> <631174203.307923.1559632166677@mail.yahoo.com> Message-ID: <1559657452533-0.post@n2.nabble.com> Thank You for your response. -- Sent from: http://itk-insight-users.2283740.n2.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 From srbn.ghosh99 at gmail.com Tue Jun 4 10:38:35 2019 From: srbn.ghosh99 at gmail.com (Shrabani Ghosh) Date: Tue, 4 Jun 2019 07:38:35 -0700 (MST) Subject: [ITK] [ITK-users] Registration-- Mutual Information based for CT to CT 3D data In-Reply-To: <631174203.307923.1559632166677@mail.yahoo.com> References: <1559602355207-0.post@n2.nabble.com> <631174203.307923.1559632166677@mail.yahoo.com> Message-ID: <1559659115497-0.post@n2.nabble.com> There are lots of modules under elastix. Which module should I use for CT to CT registration? -- Sent from: http://itk-insight-users.2283740.n2.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 From coyarzunlaura at googlemail.com Fri Jun 14 09:07:28 2019 From: coyarzunlaura at googlemail.com (Cristina Oyarzun) Date: Fri, 14 Jun 2019 15:07:28 +0200 Subject: [ITK] [ITK-users] CFP: MICCAI CLIP 2019: Clinical Image-based Procedures: Towards Holistic Patient Models for Personalised Healthcare Message-ID: CALL FOR PAPERS MICCAI 2019 Workshop on Clinical Image-based Procedures: Towards Holistic Patient Models for Personalised Healthcare October 17, 2019 Shenzhen, China Website:http://miccai-clip.org/ ============================== ========================================== SCOPE CLIP is about the effective translation of computational image-based techniques into the clinic filling the gaps between medical imaging, basic science and clinical applications. As it nowadays becomes more and more important for many clinical applications to base decisions not only on image data alone, a focus of CLIP 2019 is on the creation of holistic patient models. Here, image data such as radiologic images, microscopy images, and photographs is combined with non-image information such as ?omics? data (e.g. genomics, proteomics), life style data, demographics, EEG, and other to build a more complete picture of the individual patient and to subsequently provide better diagnosis and therapies. CLIP 2019 provides a forum for work centered on specific clinical applications, including techniques and procedures based on comprehensive clinical image and other data. Submissions related to applications already in use and evaluated by clinical users are particularly encouraged. We explicitly welcome novel techniques and applications that are looking at combining image analysis with clinical data mining and analytics, user studies, and other heterogeneous data. TOPICS * Combination of image analysis with other heterogeneous data including radiography images, microscopy, photographs, genomics, proteomics, life style data, EEG, bio-data, and other * Multimodal image integration for modeling, planning and guidance * Strategies for patient-specific and anatomical modeling to support planning and interventions * Clinical studies employing advanced image-guided methods * Clinical translation and validation of image-guided systems * Current challenges and emerging techniques in image-based procedures * Clinical applications in open and minimally invasive procedures PAPER SUBMISSION Papers can be up to 10 pages. All submissions will be peer-reviewed by at least 3 members of the program committee. Reviewing is double-blind so authors have to prepare their manuscripts such that their identity cannot be derived from their submission. The selection of papers will be based on the significance of results, novelty, technical merit, relevance and clarity of presentation. Electronic paper proceedings will be arranged. The papers will be published in a Springer Lecture Notes in Computer Science (LNCS) proceeding. LNCS is indexed by Scopus, ACM Digital Library, DBLP, Conference Proceedings Citation Index (part of Clarivate Analytics? Web of Science), and others. WORKSHOP FORMAT Papers will be presented in a day long single track workshop starting with plenary sessions. The final program will consist of previously unpublished and contributed papers with substantial time allocated to discussion. A poster session will accommodate further discussion on new ideas. IMPORTANT DATES * July 15, 2019: Paper submission due date * August 1, 2019: Notification of acceptance * tbd: Final camera-ready paper submission deadline CONTACT Inquires about the workshop should be sent to the Information Desk ( info at miccai-clip.org). ORGANIZERS (in alphabetical order) Klaus Drechsler (Fraunhofer IGD, Germany) Marius Erdt (Fraunhofer IDM at NTU, Singapore) Miguel Gonz?lez Ballester (ICREA - Universitat Pompeu Fabra, Spain) Marius George Linguraru (Children's National Medical Center, USA) Cristina Oyarzun Laura (Fraunhofer IGD, Germany) Raj Shekhar (Children's National Medical Center, USA) Stefan Wesarg (Fraunhofer IGD, Germany) -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- 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 gabriele.belotti at mail.polimi.it Mon Jun 17 09:00:54 2019 From: gabriele.belotti at mail.polimi.it (Gabriele Belotti) Date: Mon, 17 Jun 2019 13:00:54 +0000 Subject: [ITK] [ITK-users] TwoProjectionRegistration Message-ID: Dear all, I'm testing this particular module to evaluate a 2D/3D registration context. I was able to obtain DRRs using Siddon-Jacobs ray tracing method (starting point is an FDK of POPI model) and as a proof of concept I fed two of these resulting projections (first at the correct angles and centering, then at small tilted angles with added displacement to the CT volume center). What I noticed is that the computation of a single step in the registration is incredibly slow even in the case where the initial transform is already at the correct position (around 60"). I think the long computation times are possibly caused by metric calculation on the 2 Projections vs the DRRs generated from the volume by the interpolators (Siddon-Jacobs), but I cannot verify this assumption since I can only observe a full registration step. Is there a way to speed up the process? Unfortunately the custom classes that were implemented in this module do not come with many useful tools such as a Sampling Strategy. Thanks to anyone contributing -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- 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 dzenanz at gmail.com Mon Jun 17 09:58:39 2019 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 17 Jun 2019 09:58:39 -0400 Subject: [ITK] [ITK-users] TwoProjectionRegistration In-Reply-To: References: Message-ID: Hi Gabriele, we have migrated away from this mailing list and to the forum . Please repost your question there. Regards, D?enan On Mon, Jun 17, 2019 at 9:01 AM Gabriele Belotti < gabriele.belotti at mail.polimi.it> wrote: > Dear all, > > I?m testing this particular module to evaluate a 2D/3D registration > context. > I was able to obtain DRRs using Siddon-Jacobs ray tracing method (starting > point is an FDK of POPI model) and as a proof of concept I fed two of these > resulting projections (first at the correct angles and centering, then at > small tilted angles with added displacement to the CT volume center). > What I noticed is that the computation of a single step in the > registration is incredibly slow even in the case where the initial > transform is already at the correct position (around 60?). > I think the long computation times are possibly caused by metric > calculation on the 2 Projections vs the DRRs generated from the volume by > the interpolators (Siddon-Jacobs), but I cannot verify this assumption > since I can only observe a full registration step. > > Is there a way to speed up the process? Unfortunately the custom classes > that were implemented in this module do not come with many useful tools > such as a Sampling Strategy. > > Thanks to anyone contributing > 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: -------------- next part -------------- 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 srbn.ghosh99 at gmail.com Mon Jun 24 13:45:22 2019 From: srbn.ghosh99 at gmail.com (Shrabani Ghosh) Date: Mon, 24 Jun 2019 10:45:22 -0700 (MST) Subject: [ITK] [ITK-users] 3D volume of Stacked 2D images have different size from the 2D images Message-ID: <1561398322361-0.post@n2.nabble.com> Hi, I have stacked all the 2D slices of the images. But the 3D volume I am getting has different height-width than the 2D images. The snapshot is the size of one 2D image and outline of 3D volume. How is it changing the sizes? Here is my create3Dvolume code: #include "itkImage.h" #include "itkImageFileReader.h" #include "itkImageFileWriter.h" #include "itkTileImageFilter.h" #include #include #include #include using namespace std; using namespace boost::filesystem; int main(int argc, const char* argv[]) { int x; int j = 1; const unsigned int InputDimension = 3; const unsigned int OutputDimension = 3; typedef unsigned char PixelType; typedef itk::Image< PixelType, InputDimension > InputImageType; typedef itk::Image< PixelType, OutputDimension > OutputImageType; typedef itk::ImageFileReader< InputImageType > ReaderType; ReaderType::Pointer reader = ReaderType::New(); typedef itk::TileImageFilter< InputImageType, OutputImageType > FilterType; FilterType::Pointer filter = FilterType::New(); itk::FixedArray< unsigned int, OutputDimension > layout; layout[0] = 1; layout[1] = 1; layout[2] = 0; filter->SetLayout(layout); std::string s ; path p("E:\\Programs\\Extract2dfrom3d\\ctmoving1"); { if (!is_directory(ii->path())) //we eliminate directories { // if (j == 20) break; s = ii->path().string(); reader->SetFileName(s.c_str()); } try { reader->Update(); } catch (itk::ExceptionObject & e) { std::cerr << e << std::endl; getchar(); return EXIT_FAILURE; } InputImageType::Pointer input = reader->GetOutput(); input->DisconnectPipeline(); filter->SetInput(j - 1, input); } const PixelType defaultValue = 0; filter->SetDefaultPixelValue(defaultValue); typedef itk::ImageFileWriter< OutputImageType > WriterType; WriterType::Pointer writer = WriterType::New(); writer->SetFileName("E:\\Programs\\Extract2dfrom3d\\ctmoving1\\ctmoving1.mhd"); writer->SetInput(filter->GetOutput()); writer->Update(); try { writer->Update(); } catch (itk::ExceptionObject & error) { std::cerr << "Error: " << error << std::endl; std::cin >> x; return EXIT_FAILURE; } return EXIT_SUCCESS; } Thank You -- Sent from: http://itk-insight-users.2283740.n2.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 From dzenanz at gmail.com Sun Jun 30 10:48:54 2019 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Sun, 30 Jun 2019 10:48:54 -0400 Subject: [ITK] [ITK-users] 3D volume of Stacked 2D images have different size from the 2D images In-Reply-To: <980166110.93692.1561419311751.JavaMail.administrator@n2.nabble.com> References: <980166110.93692.1561419311751.JavaMail.administrator@n2.nabble.com> Message-ID: Please repost this question on the forum . Regards, D?enan On Mon, Jun 24, 2019 at 7:35 PM wrote: > Hi, > > I have stacked resampled 2D slices of the images. Like the original is > 512x546x94 and after resample it becomes 340x339x94. But when I open them > in paraview, they both have the same size of outline. How is it not > changing the sizes? > > > > _____________________________________ > Sent from http://itk-insight-users.2283740.n2.nabble.com > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- 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