From dzenanz at gmail.com Fri Mar 2 10:41:10 2018 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 2 Mar 2018 10:41:10 -0500 Subject: [ITK] Query regarding implementation of itkGeometricJacobianDeterminantImageFilter.hxx In-Reply-To: References: Message-ID: Hi Mageshwar, we have moved to discourse forum. Please repost your question there. Regards, D?enan On Wed, Feb 28, 2018 at 10:34 AM, Mageshwar Selvakumar < mageshwar.selvakumar at outlook.com> wrote: > Dear ITK community members, > > I want to have a deeper insight into the implementation of jacobian > determinant in itkGeometricJacobianDeterminantImageFilter.hxx, but I'm > unable to find some theory which explains on what basis this code is > implemented. It would be nice if someone could refer some books or > literature on jacobian implementation, especially the method used here, the > connection between triangular area and tetrahedral volume computation and > jacobian determinant. It would be of a great help to me, if someone > can direct me towards it. > > Thank you, > > Kind regards > > Mageshwar Selvakumar, M.Sc > > > Department of Pharmakologische Bildgebung und Bildanalyse > > Friedrich Alexander Universit?t Erlangen N?rnberg > > > Office: Fahrstr. 17, 91054 Erlangen > > Phone: + 49-9131-8522898 > > > > The ITK community is transitioning from this mailing list to > discourse.itk.org. Please join us there! > ________________________________________ > Community mailing list > Community at itk.org > https://itk.org/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Fri Mar 2 10:48:58 2018 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 2 Mar 2018 10:48:58 -0500 Subject: [ITK] [ITK-users] object orientation detection In-Reply-To: <1903632477.9254637.1520004045990@mail.yahoo.com> References: <1903632477.9254637.1520004045990.ref@mail.yahoo.com> <1903632477.9254637.1520004045990@mail.yahoo.com> Message-ID: Hi Majid, we have moved to discourse forum. Reposting your question there might yield more answers. Finding orientation of an arbitrary object depends a lot on the shape of the object and the surrounding background image content. There is a 2D and 3D skeletonization filter. You might try objectness and vesselenss filters. Regards, D?enan On Fri, Mar 2, 2018 at 10:20 AM, Majid M. Sadeghi via Insight-users < insight-users at itk.org> wrote: > Dear All, > > I have a 3D object which is located in an arbitrary position and > orientation in the space. My goal is to roughly find the orientation of the > object. > > To achieve that, I think I need a descriptor of the object to define it. > For that descriptor I am thinking maybe a skeleton of the object will work, > since my object?s shape is a specific shape with certain twists and corners. > > After having the descriptor I need to be able to find the orientation of > the descriptor. And for this I am thinking I might be able to use certain > relationships of points located on the skeleton, with each other or with > the origin of the space. > > So my questions are: > > 1. Is there a better method to do this? (Finding the orientation of an > object) > > 2. Is there a method in VTK/ITK to extract the skeleton of an object? > > 3. Is there any other descriptor available in VTK/ITK which might be > helpful? > > 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: -------------- 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 M.Varga at brighton.ac.uk Mon Mar 5 12:11:48 2018 From: M.Varga at brighton.ac.uk (Matyas Varga) Date: Mon, 5 Mar 2018 17:11:48 +0000 Subject: [ITK] analysing scans other than brain Message-ID: Dear ITK, I was wondering if it was possible to analyse (surface-based morphometry and SPM) NOT brain scans. I am doing my PhD looking at how the shape of children's feet change as they get older (2-7 years old). I will use a 3D scanner which will provide me with a mesh of triangles of the foot and I am considering to create average age group foot shapes and compare them using surface based morphometry and SPM. I will obviously have to create my own foot "atlas". I was wondering if this was possible in ITK? Please let me know if it is possible or if you have any suggestions if it is not. Thank you. Best Regards Matyas Varga PhD student School of Health Sciences Research University of Brighton Aldro Building, 49 Darley Road Eastbourne, BN20 7UR Tel: 01273 644189 ___________________________________________________________ This email has been scanned by MessageLabs' Email Security System on behalf of the University of Brighton. For more information see: https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Mon Mar 5 13:03:27 2018 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 5 Mar 2018 13:03:27 -0500 Subject: [ITK] analysing scans other than brain In-Reply-To: References: Message-ID: Hi Matyas, you could check out SlicerSalt and Slicer's forum . Posting on ITK's forum might help as well. Regards, D?enan On Mon, Mar 5, 2018 at 12:11 PM, Matyas Varga wrote: > Dear ITK, > > > > I was wondering if it was possible to analyse (surface-based morphometry > and SPM) NOT brain scans. > > I am doing my PhD looking at how the shape of children?s feet change as > they get older (2-7 years old). > > > > I will use a 3D scanner which will provide me with a mesh of triangles of > the foot and I am considering to create average age group foot shapes and > compare them using surface based morphometry and SPM. > > I will obviously have to create my own foot ?atlas?. I was wondering if > this was possible in ITK? > > > > Please let me know if it is possible or if you have any suggestions if it > is not. > > > > Thank you. > > > > Best Regards > > > > Matyas Varga > > PhD student > > School of Health Sciences Research > > University of Brighton > > Aldro Building, 49 Darley Road > > Eastbourne, BN20 7UR > > Tel: 01273 644189 > > > > > > ___________________________________________________________ > This email has been scanned by MessageLabs' Email Security System > on behalf of the University of Brighton. For more information see: > https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx > > The ITK community is transitioning from this mailing list to > discourse.itk.org. Please join us there! > ________________________________________ > Community mailing list > Community at itk.org > https://itk.org/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From samuel.gerber at kitware.com Mon Mar 5 13:08:50 2018 From: samuel.gerber at kitware.com (Samuel Gerber) Date: Mon, 5 Mar 2018 13:08:50 -0500 Subject: [ITK] analysing scans other than brain In-Reply-To: References: Message-ID: Something to look into might be deformetrica: http://www.deformetrica.org Cheers Sam On Mar 5, 2018 12:25 PM, "Matyas Varga" wrote: > Dear ITK, > > > > I was wondering if it was possible to analyse (surface-based morphometry > and SPM) NOT brain scans. > > I am doing my PhD looking at how the shape of children?s feet change as > they get older (2-7 years old). > > > > I will use a 3D scanner which will provide me with a mesh of triangles of > the foot and I am considering to create average age group foot shapes and > compare them using surface based morphometry and SPM. > > I will obviously have to create my own foot ?atlas?. I was wondering if > this was possible in ITK? > > > > Please let me know if it is possible or if you have any suggestions if it > is not. > > > > Thank you. > > > > Best Regards > > > > Matyas Varga > > PhD student > > School of Health Sciences Research > > University of Brighton > > Aldro Building, 49 Darley Road > > Eastbourne, BN20 7UR > > Tel: 01273 644189 > > > > > > ___________________________________________________________ > This email has been scanned by MessageLabs' Email Security System > on behalf of the University of Brighton. For more information see: > https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx > > The ITK community is transitioning from this mailing list to > discourse.itk.org. Please join us there! > ________________________________________ > Community mailing list > Community at itk.org > https://itk.org/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From M.Varga at brighton.ac.uk Tue Mar 6 07:24:03 2018 From: M.Varga at brighton.ac.uk (Matyas Varga) Date: Tue, 6 Mar 2018 12:24:03 +0000 Subject: [ITK] reading mesh in ITK Message-ID: Hi, Is it possible to read mesh files (OBJ, PLY, WRL, STL, AOP, ASCII, Disney PTEX, E57, XYZRGB files.) in ITK? Thank you. Best Regards Matyas Varga ___________________________________________________________ This email has been scanned by MessageLabs' Email Security System on behalf of the University of Brighton. For more information see: https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx -------------- next part -------------- An HTML attachment was scrubbed... URL: From jhlegarreta at vicomtech.org Tue Mar 6 07:50:54 2018 From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta) Date: Tue, 6 Mar 2018 13:50:54 +0100 Subject: [ITK] reading mesh in ITK In-Reply-To: References: Message-ID: Dear Matyas, it is; you may want to have a look at the related examples: https://itk.org/ITKExamples/src/Core/Mesh/index.html However, VTK offers broader capabilities to deal with meshes. Also note that the ITK discussion has transitioned from this mailing list to discourse.itk.org. Posting there is likely to reach a broader audience. HTH, JON HAITZ -- On 6 March 2018 at 13:24, Matyas Varga wrote: > Hi, > > > > Is it possible to read mesh files (OBJ, PLY, WRL, STL, AOP, ASCII, Disney > PTEX, E57, XYZRGB files.) in ITK? > > > > Thank you. > > > > Best Regards > > > > Matyas Varga > > > > > ___________________________________________________________ > This email has been scanned by MessageLabs' Email Security System > on behalf of the University of Brighton. For more information see: > https://staff.brighton.ac.uk/is/computing/Pages/Email/spam.aspx > > The ITK community is transitioning from this mailing list to > discourse.itk.org. Please join us there! > ________________________________________ > Community mailing list > Community at itk.org > https://itk.org/mailman/listinfo/community > From srbn.ghosh99 at gmail.com Thu Mar 8 15:07:24 2018 From: srbn.ghosh99 at gmail.com (Shrabani Ghosh) Date: Thu, 8 Mar 2018 13:07:24 -0700 (MST) Subject: [ITK] [ITK-users] 3D image picking specific location voxel value Message-ID: <1520539644234-0.post@n2.nabble.com> I have a 3D image . I want to go to the specific location of the image. and want to pick the voxel value. How I can I do that? Like in this picture I want go to the exact red color location. This in one slice of the 3D image. In the program, Can I go to specific slice and go to specific location? -- 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 Thu Mar 8 16:44:58 2018 From: srbn.ghosh99 at gmail.com (Shrabani Ghosh) Date: Thu, 8 Mar 2018 14:44:58 -0700 (MST) Subject: [ITK] [ITK-users] ITK registration Message-ID: <1520545498684-0.post@n2.nabble.com> I have a 3D image volume. And I have 2d segmented image . I need to do the registration using 3d image specific slice and 2d segmented image. Any registration example does that? -- 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 Fri Mar 9 09:05:56 2018 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 9 Mar 2018 09:05:56 -0500 Subject: [ITK] [ITK-users] 3D image picking specific location voxel value In-Reply-To: <1520539644234-0.post@n2.nabble.com> References: <1520539644234-0.post@n2.nabble.com> Message-ID: Hi Shrabani, to read a specific location in an image, you should use GetPixel() method. There is an example of using SetPixel() which is very similar. Regards, D?enan On Thu, Mar 8, 2018 at 3:07 PM, Shrabani Ghosh wrote: > I have a 3D image . I want to go to the specific location of the image. > and > want to pick the voxel value. How I can I do that? > > > Like in this picture I want go to the exact red color location. This in one > slice of the 3D image. > In the program, Can I go to specific slice and go to specific location? > > > > -- > 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 > -------------- 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 Fri Mar 9 09:16:35 2018 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 9 Mar 2018 09:16:35 -0500 Subject: [ITK] [ITK-users] ITK registration In-Reply-To: <1520545498684-0.post@n2.nabble.com> References: <1520545498684-0.post@n2.nabble.com> Message-ID: Hi Shrabani, if I understand correctly, you need to extract a specific slice from a 3D image and then do classic 2D registration using that slice? Extract filter's documentation. Extract example . 2D registration example . You should post further question on the forum , to which this mailing list has transitioned. Regards, D?enan On Thu, Mar 8, 2018 at 4:44 PM, Shrabani Ghosh wrote: > I have a 3D image volume. And I have 2d segmented image . I need to do the > registration using 3d image specific slice and 2d segmented image. Any > registration example does that? > > > > -- > 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 > -------------- 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 Fri Mar 9 12:15:03 2018 From: srbn.ghosh99 at gmail.com (Shrabani Ghosh) Date: Fri, 9 Mar 2018 12:15:03 -0500 Subject: [ITK] [ITK-users] ITK registration In-Reply-To: References: <1520545498684-0.post@n2.nabble.com> Message-ID: does the registration creates problem if the file sizes are so diff? LIke in my case the two files are these. I want to register the right( red )image on a specific location of the left image. On Fri, Mar 9, 2018 at 9:16 AM, D?enan Zuki? wrote: > Hi Shrabani, > > if I understand correctly, you need to extract a specific slice from a 3D > image and then do classic 2D registration using that slice? > > Extract > filter's documentation. Extract example > . > 2D registration example > > . > > You should post further question on the forum , > to which this mailing list has transitioned. > > Regards, > D?enan > > On Thu, Mar 8, 2018 at 4:44 PM, Shrabani Ghosh > wrote: > >> I have a 3D image volume. And I have 2d segmented image . I need to do the >> registration using 3d image specific slice and 2d segmented image. Any >> registration example does that? >> >> >> >> -- >> 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 >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: axgreaterpalatineforamen0004.png Type: image/png Size: 474 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ax ct0004.png Type: image/png Size: 185676 bytes Desc: not available 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 bakkari.abdelkhalek at hotmail.fr Fri Mar 9 13:51:12 2018 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Fri, 9 Mar 2018 18:51:12 +0000 Subject: [ITK] [ITK-users] initial contour/surface as the zero level set Message-ID: Dear All, I am trying to adopt the eodesicActiveContourLevelSetImage Filter. However, I don?t know how to create the initial contour/surface using ITK and Qt. Could you please help me? Kind regards, -------------- 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 c.spanakis83 at gmail.com Tue Mar 13 06:22:21 2018 From: c.spanakis83 at gmail.com (Constantinus Spanakis) Date: Tue, 13 Mar 2018 12:22:21 +0200 Subject: [ITK] Image registration when Images have different size Message-ID: Hello. I want to register two images which have different size. What I want to do is rigid registration, but the images have different size. Is it possible to register them? Thank you in advance -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Tue Mar 13 10:00:48 2018 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 13 Mar 2018 10:00:48 -0400 Subject: [ITK] Image registration when Images have different size In-Reply-To: References: Message-ID: Hi Constantinus, if they have different pixel size but same physical size (due to different image spacing), you can input them into rigid registration examples directly. If not, you might want to use similarity or affine transform instead of rigid. Regards, D?enan On Tue, Mar 13, 2018 at 6:22 AM, Constantinus Spanakis < c.spanakis83 at gmail.com> wrote: > Hello. I want to register two images which have different size. What I > want to do is rigid registration, but the images have different size. Is it > possible to register them? > > Thank you in advance > > The ITK community is transitioning from this mailing list to > discourse.itk.org. Please join us there! > ________________________________________ > Community mailing list > Community at itk.org > https://itk.org/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Wed Mar 14 14:33:10 2018 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Wed, 14 Mar 2018 18:33:10 +0000 Subject: [ITK] [ANNOUNCE] SimpleITK 1.1 Release Candidate 2 Message-ID: We are pleased to announce the SimpleITK 1.1 Release Candidate 2! For more information please see the ITK discourse thread: https://discourse.itk.org/t/simpleitk-1-1-release-candidate-2/771 -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Wed Mar 14 16:14:08 2018 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 14 Mar 2018 16:14:08 -0400 Subject: [ITK] Hackathon Following WBIR Message-ID: Leiden, The Netherlands June 28 & 29, 2018 Website: wbir2018.nl New: Call for 1-page abstracts: deadline April 1, 2018 New: Continuous Registration Challenge ? Participate! New: Post-WBIR Hackathon Dear colleagues, We have some exciting updates on the 8th International Workshop on Biomedical Image Registration, WBIR2018, held in Leiden, the Netherlands. For more info, please visit our website https://wbir2018.nl. We have a draft program online (confirmed keynote speech by Prof.dr. Max Welling, authority on machine learning!), and you may now register to attend the conference! CALL FOR 1-PAGE ABSTRACTS Missed the full paper submission deadline, but still want to participate? Submit a 1-page abstract by April 1! Abstracts will undergo a (mild) single-blind review and will be presented as posters (including a 2-minute plenary pitch) at the conference, but will not appear in the proceedings. We are excited to hear about your latest technical breakthroughs, clinical application studies, and also welcome abstracts of recently published or submitted journal papers. CONTINUOUS REGISTRATION CHALLENGE WBIR2018 will include a special session on the Continuous Registration Challenge (CRC). CRC is a new collaborative software platform for medical image registration. Please check it out at https://continuousregistration.grand-challenge.org, attend one of the weekly webinars, and participate! Post-WBIR Hackathon In collaboration with the Insight Toolkit (ITK) community and Kitware, we will host a hackathon on the day after the main conference (June 30). Participation is free of charge. IMPORTANT DATES ? Camera ready: March 23, 2018 ? 1-page abstract submission: April 1, 2018 ? Notification for 1-page abstracts: April 10, 2018 ? Early-bird registration deadline May 1, 2018 ? Conference: June 28/29, 2018 ? Post-WBIR Hackathon June 30, 2018 SCOPE Submissions are invited in all areas of biomedical image registration. Topics of interest include, but are not limited to: ? Novel registration methodology: 2D/3D/4D, spatiotemporal/dynamic, slice-to-volume, projective, single/multi-modal, intra/inter-subject, shape registration, model-based, patch-based, multi-channel, tracking, real-time, similarity measures, machine learning / deep learning techniques ? Mathematical aspects of image registration: continuous/discrete optimization methods, diffeomorphisms, LDDMM, stationary velocity, inverse consistency, multi-scale ? Biomedical applications of registration: computer-assisted interventions, image-guided therapy, treatment planning/delivery, diagnosis/prognosis, atlas-based segmentation, label fusion, histopathology correlation, motion-compensated reconstruction, serial studies, morphometry, biomechanics, image retrieval/restoration/fusion, imaging biomarkers for precision medicine, radiomics & radiogenomics ? Early proof of concept, with potential use in biomedical applications ? Validation of registration: quantitative and qualitative methods, benchmarking, comparison studies, phantom studies, correlation to outcome The conference papers will be published in the Lecture Notes in Computer Science (LNCS). ORGANIZING COMMITTEE Stefan Klein - Erasmus MC, The Netherlands Marius Staring - Leiden University Medical Center, The Netherlands Stanley Durrleman - INRIA/ICM ARAMIS Lab, France Stefan Sommer - University of Copenhagen, Denmark From mrguilfoyle at gmail.com Wed Mar 14 17:23:37 2018 From: mrguilfoyle at gmail.com (Mathew Guilfoyle) Date: Wed, 14 Mar 2018 21:23:37 +0000 Subject: [ITK] SimpleITK CoherenceEnhancingDiffusionImage Filter In-Reply-To: References: Message-ID: The release notes for 1.1rc2 mention 'optional wrapping' of CoherenceEnhancingDiffusionImage Filter. I can't see a CMake option to include this filter when running the Superbuild and it's not available after successfully compiling the release with standard options. Is there a way of turning on wrapping of this filter? Thanks > On 14 Mar 2018, at 18:33, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote: > > We are pleased to announce the SimpleITK 1.1 Release Candidate 2! > > For more information please see the ITK discourse thread: > https://discourse.itk.org/t/simpleitk-1-1-release-candidate-2/771 > 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 -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1380 bytes Desc: not available URL: From dzenanz at gmail.com Fri Mar 16 16:12:24 2018 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 16 Mar 2018 16:12:24 -0400 Subject: [ITK] [ITK-users] ITK registration In-Reply-To: References: <1520545498684-0.post@n2.nabble.com> Message-ID: Hi Shrabani, I can't shake the feeling that you are trying to do something unnecessary. You should not need to register an image with a segmentation! You might only need to adjust reference frames if they are different. Moreover, you are trying to register a 3D image with a 2D registration. I fail to see the point of that - that's why I misunderstood your initial question. Can you post your question to the forum , and give a more detailed description of the problem and its background? Most importantly: why do you need to do it? Regards, D?enan On Fri, Mar 16, 2018 at 3:04 PM, Shrabani Ghosh wrote: > But when I am trying to register, I cannot do it. I dont is it the reason > of the size difference? the left image is 512x546 and the right image is > 105x37. > > On Fri, Mar 9, 2018 at 12:15 PM, Shrabani Ghosh > wrote: > >> does the registration creates problem if the file sizes are so diff? LIke >> in my case the two files are these. I want to register the right( red >> )image on a specific location of the left image. >> >> >> >> >> On Fri, Mar 9, 2018 at 9:16 AM, D?enan Zuki? wrote: >> >>> Hi Shrabani, >>> >>> if I understand correctly, you need to extract a specific slice from a >>> 3D image and then do classic 2D registration using that slice? >>> >>> Extract >>> >>> filter's documentation. Extract example >>> . >>> 2D registration example >>> >>> . >>> >>> You should post further question on the forum >>> , to which this mailing list has >>> transitioned. >>> >>> Regards, >>> D?enan >>> >>> On Thu, Mar 8, 2018 at 4:44 PM, Shrabani Ghosh >>> wrote: >>> >>>> I have a 3D image volume. And I have 2d segmented image . I need to do >>>> the >>>> registration using 3d image specific slice and 2d segmented image. Any >>>> registration example does that? >>>> >>>> >>>> >>>> -- >>>> 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 >>>> >>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ax ct0004.png Type: image/png Size: 185676 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: axgreaterpalatineforamen0004.png Type: image/png Size: 474 bytes Desc: not available 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 Fri Mar 16 16:52:45 2018 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 16 Mar 2018 16:52:45 -0400 Subject: [ITK] [ITK-users] ITK registration In-Reply-To: References: <1520545498684-0.post@n2.nabble.com> Message-ID: You need to know the relationship between reference frames of the images (e.g. translation, rotation etc) in order to adjust one image to the other. And you seem to be missing that information. On Fri, Mar 16, 2018 at 4:37 PM, Shrabani Ghosh wrote: > Now I am trying to do with extracting a 2D slice from 3D image and > register with the segmented image. I need to register it because after the > registration I will label on ct image with registered image. > How to adjust reference frames if i want to do it? > > On Fri, Mar 16, 2018 at 4:12 PM, D?enan Zuki? wrote: > >> Hi Shrabani, >> >> I can't shake the feeling that you are trying to do something >> unnecessary. You should not need to register an image with a segmentation! >> You might only need to adjust reference frames if they are different. >> Moreover, you are trying to register a 3D image with a 2D registration. I >> fail to see the point of that - that's why I misunderstood your initial >> question. Can you post your question to the forum >> , and give a more detailed description of >> the problem and its background? Most importantly: why do you need to do it? >> >> Regards, >> D?enan >> >> On Fri, Mar 16, 2018 at 3:04 PM, Shrabani Ghosh >> wrote: >> >>> But when I am trying to register, I cannot do it. I dont is it the >>> reason of the size difference? the left image is 512x546 and the right >>> image is 105x37. >>> >>> On Fri, Mar 9, 2018 at 12:15 PM, Shrabani Ghosh >>> wrote: >>> >>>> does the registration creates problem if the file sizes are so diff? >>>> LIke in my case the two files are these. I want to register the right( red >>>> )image on a specific location of the left image. >>>> >>>> >>>> >>>> >>>> On Fri, Mar 9, 2018 at 9:16 AM, D?enan Zuki? wrote: >>>> >>>>> Hi Shrabani, >>>>> >>>>> if I understand correctly, you need to extract a specific slice from a >>>>> 3D image and then do classic 2D registration using that slice? >>>>> >>>>> Extract >>>>> >>>>> filter's documentation. Extract example >>>>> . >>>>> 2D registration example >>>>> >>>>> . >>>>> >>>>> You should post further question on the forum >>>>> , to which this mailing list has >>>>> transitioned. >>>>> >>>>> Regards, >>>>> D?enan >>>>> >>>>> On Thu, Mar 8, 2018 at 4:44 PM, Shrabani Ghosh >>>> > wrote: >>>>> >>>>>> I have a 3D image volume. And I have 2d segmented image . I need to >>>>>> do the >>>>>> registration using 3d image specific slice and 2d segmented image. Any >>>>>> registration example does that? >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> 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 >>>>>> >>>>> >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: axgreaterpalatineforamen0004.png Type: image/png Size: 474 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ax ct0004.png Type: image/png Size: 185676 bytes Desc: not available 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 Fri Mar 16 17:26:02 2018 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 16 Mar 2018 17:26:02 -0400 Subject: [ITK] [ITK-users] ITK registration In-Reply-To: References: <1520545498684-0.post@n2.nabble.com> Message-ID: You can add translation to (or subtract from) image origin . And that should be it. No registration needed. This example might be of some use. Regards, D?enan On Fri, Mar 16, 2018 at 5:09 PM, Shrabani Ghosh wrote: > Yes. I have the translation information. how to adjust with the > translation information ? > > On Fri, Mar 16, 2018 at 4:52 PM, D?enan Zuki? wrote: > >> You need to know the relationship between reference frames of the images >> (e.g. translation, rotation etc) in order to adjust one image to the other. >> And you seem to be missing that information. >> >> On Fri, Mar 16, 2018 at 4:37 PM, Shrabani Ghosh >> wrote: >> >>> Now I am trying to do with extracting a 2D slice from 3D image and >>> register with the segmented image. I need to register it because after the >>> registration I will label on ct image with registered image. >>> How to adjust reference frames if i want to do it? >>> >>> On Fri, Mar 16, 2018 at 4:12 PM, D?enan Zuki? wrote: >>> >>>> Hi Shrabani, >>>> >>>> I can't shake the feeling that you are trying to do something >>>> unnecessary. You should not need to register an image with a segmentation! >>>> You might only need to adjust reference frames if they are different. >>>> Moreover, you are trying to register a 3D image with a 2D registration. I >>>> fail to see the point of that - that's why I misunderstood your initial >>>> question. Can you post your question to the forum >>>> , and give a more detailed description of >>>> the problem and its background? Most importantly: why do you need to do it? >>>> >>>> Regards, >>>> D?enan >>>> >>>> On Fri, Mar 16, 2018 at 3:04 PM, Shrabani Ghosh >>> > wrote: >>>> >>>>> But when I am trying to register, I cannot do it. I dont is it the >>>>> reason of the size difference? the left image is 512x546 and the right >>>>> image is 105x37. >>>>> >>>>> On Fri, Mar 9, 2018 at 12:15 PM, Shrabani Ghosh < >>>>> srbn.ghosh99 at gmail.com> wrote: >>>>> >>>>>> does the registration creates problem if the file sizes are so diff? >>>>>> LIke in my case the two files are these. I want to register the right( red >>>>>> )image on a specific location of the left image. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Fri, Mar 9, 2018 at 9:16 AM, D?enan Zuki? >>>>>> wrote: >>>>>> >>>>>>> Hi Shrabani, >>>>>>> >>>>>>> if I understand correctly, you need to extract a specific slice from >>>>>>> a 3D image and then do classic 2D registration using that slice? >>>>>>> >>>>>>> Extract >>>>>>> >>>>>>> filter's documentation. Extract example >>>>>>> . >>>>>>> 2D registration example >>>>>>> >>>>>>> . >>>>>>> >>>>>>> You should post further question on the forum >>>>>>> , to which this mailing list has >>>>>>> transitioned. >>>>>>> >>>>>>> Regards, >>>>>>> D?enan >>>>>>> >>>>>>> On Thu, Mar 8, 2018 at 4:44 PM, Shrabani Ghosh < >>>>>>> srbn.ghosh99 at gmail.com> wrote: >>>>>>> >>>>>>>> I have a 3D image volume. And I have 2d segmented image . I need to >>>>>>>> do the >>>>>>>> registration using 3d image specific slice and 2d segmented image. >>>>>>>> Any >>>>>>>> registration example does that? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> 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 >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: axgreaterpalatineforamen0004.png Type: image/png Size: 474 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ax ct0004.png Type: image/png Size: 185676 bytes Desc: not available 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 blowekamp at mail.nih.gov Tue Mar 20 13:11:32 2018 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Tue, 20 Mar 2018 17:11:32 +0000 Subject: [ITK] SimpleITK CoherenceEnhancingDiffusionImage Filter In-Reply-To: References: Message-ID: Hello, Sorry I missed this e-mail, it got automatically marked as junk ( I suggest joining ITK discourse for discussing ITK and SimpleITK. To enable this additional filter in the SimpleITK Superbuild, the ITK remote module needs to be enabled. You can either add "-DModule_AnisotropicDiffusionLBR:BOOL=ON" on the command line or from the CMake GUI press the "Add Entry" button and add the "Module_AnisotropicDiffusionLBR" as a bool variable. Other remote modules can be enabled in the SimpleITK superbuild and the variable will automatically be propagated to the ITK build, those these additional filters are not wrapped. The framework to optionally wrap them is there. Contributions are welcomed. Brad ?On 3/14/18, 5:25 PM, "Mathew Guilfoyle" wrote: The release notes for 1.1rc2 mention 'optional wrapping' of CoherenceEnhancingDiffusionImage Filter. I can't see a CMake option to include this filter when running the Superbuild and it's not available after successfully compiling the release with standard options. Is there a way of turning on wrapping of this filter? Thanks > On 14 Mar 2018, at 18:33, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote: > > We are pleased to announce the SimpleITK 1.1 Release Candidate 2! > > For more information please see the ITK discourse thread: > https://discourse.itk.org/t/simpleitk-1-1-release-candidate-2/771 > 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 taylor at braun-jones.org Tue Mar 20 14:10:14 2018 From: taylor at braun-jones.org (Taylor Braun-Jones) Date: Tue, 20 Mar 2018 14:10:14 -0400 Subject: [ITK] [ITK-dev] ITK bug reporting broken? Message-ID: I'm looking at the instructions on the wiki[1] which say to go to here to obtain an account: https://issues.itk.org/jira/secure/Signup!default.jspa But the link is broken. If I try to go to the issues.itk.org address as listed on the wiki and in the [Resources > Bug Tracker] dropdown menu on itk.org, I get redirected to: https://insightsoftwareconsortium.atlassian.net/secure/Dashboard.jspa But if I click the login button on that page I get the error message: Did you use the wrong account? > Your email address taylor at braun-jones.org doesn't have access to > insightsoftwareconsortium.atlassian.net (I have an Atlassian account and am logged in) Am I doing something wrong or is ITK bug reporting broken right now? Thanks, Taylor [1] https://itk.org/Wiki/ITK/Procedure_for_Contributing_Bug_Fixes -------------- 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://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-developers From hans-johnson at uiowa.edu Tue Mar 20 14:48:54 2018 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Tue, 20 Mar 2018 18:48:54 +0000 Subject: [ITK] [ITK-dev] ITK bug reporting broken? In-Reply-To: References: Message-ID: <4C01142D-98C5-4E56-AD75-7C2524FC8BAC@uiowa.edu> An invitation has been sent to you. Hans From: Insight-developers on behalf of Taylor Braun-Jones Date: Tuesday, March 20, 2018 at 1:42 PM To: ITK Developers Subject: [ITK-dev] ITK bug reporting broken? I'm looking at the instructions on the wiki[1] which say to go to here to obtain an account: https://issues.itk.org/jira/secure/Signup!default.jspa But the link is broken. If I try to go to the issues.itk.org address as listed on the wiki and in the [Resources > Bug Tracker] dropdown menu on itk.org, I get redirected to: https://insightsoftwareconsortium.atlassian.net/secure/Dashboard.jspa But if I click the login button on that page I get the error message: Did you use the wrong account? Your email address taylor at braun-jones.org doesn't have access to insightsoftwareconsortium.atlassian.net (I have an Atlassian account and am logged in) Am I doing something wrong or is ITK bug reporting broken right now? Thanks, Taylor [1] https://itk.org/Wiki/ITK/Procedure_for_Contributing_Bug_Fixes -------------- 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://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-developers From taylor at braun-jones.org Tue Mar 20 14:59:04 2018 From: taylor at braun-jones.org (Taylor Braun-Jones) Date: Tue, 20 Mar 2018 14:59:04 -0400 Subject: [ITK] [ITK-dev] ITK bug reporting broken? In-Reply-To: <4C01142D-98C5-4E56-AD75-7C2524FC8BAC@uiowa.edu> References: <4C01142D-98C5-4E56-AD75-7C2524FC8BAC@uiowa.edu> Message-ID: Thanks, Hans. Are the wiki instructions going to be updated too so others aren't faced with the same confusing situation? On Tue, Mar 20, 2018 at 2:48 PM, Johnson, Hans J wrote: > An invitation has been sent to you. > > > > Hans > > > > > > *From: *Insight-developers on behalf > of Taylor Braun-Jones > *Date: *Tuesday, March 20, 2018 at 1:42 PM > *To: *ITK Developers > *Subject: *[ITK-dev] ITK bug reporting broken? > > > > I'm looking at the instructions on the wiki[1] which say to go to here to > obtain an account: > > > > https://issues.itk.org/jira/secure/Signup!default.jspa > > > > But the link is broken. If I try to go to the issues.itk.org address as > listed on the wiki and in the [Resources > Bug Tracker] dropdown menu on > itk.org, I get redirected to: > > > > https://insightsoftwareconsortium.atlassian.net/secure/Dashboard.jspa > > > > But if I click the login button on that page I get the error message: > > > > Did you use the wrong account? > Your email address taylor at braun-jones.org doesn't have access to > insightsoftwareconsortium.atlassian.net > > > > (I have an Atlassian account and am logged in) > > > > Am I doing something wrong or is ITK bug reporting broken right now? > > > > Thanks, > > Taylor > > > > [1] https://itk.org/Wiki/ITK/Procedure_for_Contributing_Bug_Fixes > -------------- 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://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-developers From matt.mccormick at kitware.com Tue Mar 20 15:12:43 2018 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 20 Mar 2018 15:12:43 -0400 Subject: [ITK] [ITK-dev] ITK bug reporting broken? In-Reply-To: References: <4C01142D-98C5-4E56-AD75-7C2524FC8BAC@uiowa.edu> Message-ID: I added the {{Historical}} template to the page and links to the Software Process section of the ITK Software Guide and the CONTRIBUTING.md file in the ITK repository. Thanks, Matt On Tue, Mar 20, 2018 at 2:59 PM, Taylor Braun-Jones wrote: > Thanks, Hans. Are the wiki instructions going to be updated too so others > aren't faced with the same confusing situation? > > On Tue, Mar 20, 2018 at 2:48 PM, Johnson, Hans J > wrote: >> >> An invitation has been sent to you. >> >> >> >> Hans >> >> >> >> >> >> From: Insight-developers on behalf of >> Taylor Braun-Jones >> Date: Tuesday, March 20, 2018 at 1:42 PM >> To: ITK Developers >> Subject: [ITK-dev] ITK bug reporting broken? >> >> >> >> I'm looking at the instructions on the wiki[1] which say to go to here to >> obtain an account: >> >> >> >> https://issues.itk.org/jira/secure/Signup!default.jspa >> >> >> >> But the link is broken. If I try to go to the issues.itk.org address as >> listed on the wiki and in the [Resources > Bug Tracker] dropdown menu on >> itk.org, I get redirected to: >> >> >> >> https://insightsoftwareconsortium.atlassian.net/secure/Dashboard.jspa >> >> >> >> But if I click the login button on that page I get the error message: >> >> >> >> Did you use the wrong account? >> Your email address taylor at braun-jones.org doesn't have access to >> insightsoftwareconsortium.atlassian.net >> >> >> >> (I have an Atlassian account and am logged in) >> >> >> >> Am I doing something wrong or is ITK bug reporting broken right now? >> >> >> >> Thanks, >> >> Taylor >> >> >> >> [1] https://itk.org/Wiki/ITK/Procedure_for_Contributing_Bug_Fixes > > > > 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://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-developers > 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://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-developers From matt.mccormick at kitware.com Tue Mar 27 13:48:28 2018 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 27 Mar 2018 13:48:28 -0400 Subject: [ITK] [ITK-dev] ITK Software Guide In-Reply-To: <1920304591.517234.1522172553991@mail.yahoo.com> References: <1920304591.517234.1522172553991.ref@mail.yahoo.com> <1920304591.517234.1522172553991@mail.yahoo.com> Message-ID: Hi Celina, Improvements to the Software Guide are welcome. Please see the README here on how to contribute: https://github.com/InsightSoftwareConsortium/ITKSoftwareGuide Thanks, Matt On Tue, Mar 27, 2018 at 1:42 PM, Celina Imielinska via Insight-developers < insight-developers at itk.org> wrote: > > Dear All > > (I have emailed separately Bill Schroeder at Kitware) > > I am very happy that ITK Toolkit has been thriving over so many years. > Kitware has done amazing job to maintain it and to expand it. > > Still, I am trying to contact the main co-authors of the currect ITK > Software Guide. > > I am writing about the usage of "Voronoi Region" terminology in the recent > editions of the ITK Software guide - that is very odd and not in agreement > with how Voronoi Diagram, that is one of the fundamental geometric > structures, is defined: > https://www.cs.ucsb.edu/~suri/cs235/Voronoi.pdf > > > Could you please email me - I would like to suggest that if we want to > use as "geometrical concepts associated with the ITK image" "Voronoi > region" in a form what I consider a degenerative representation of it - > then maybe it would be wise to name it differently. Not to mention the > usage of another oddity: Delaunay Region - what is it? Voronoi Diagram and > its dual, Delaunay Triangulation are classic geometric constructs that > require that the points, in the Voronoi diagram, the Voronoi points, > satisfy: > > "Non-degeneracy Condition: Assume no 4 cocircular points, and no 3 > collinear." > > This is violated in the construct included in the Guide and referred to as > Voronoi Region and Delaunay Region. > > I don't mind that the guide is not including any more my original hybrid > segmentation contribution that included Voronoi Diagram classification > https://core.ac.uk/download/pdf/27299860.pdf > I woudl like to ask you to discuss what can be done with possibly > correctingthe odd terminology, > > looking forward to hear from > > Best Regards, > > Celina Imielinska > > Celina Imielinska, PhD > Principal > Vesalius Technologies LLC > Princeton NJ > celina_imielinska at yahoo.com > 609 240 4721 <(609)%20240-4721> > > PS. old version http://www.sci.utah.edu/publications/ibanez03/ > ItkSoftwareGuide.pdf > newest https://itk.org/ItkSoftwareGuide.pdf > > 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://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-developers > > -------------- 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://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-developers From matt.mccormick at kitware.com Tue Mar 27 14:09:33 2018 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 27 Mar 2018 14:09:33 -0400 Subject: [ITK] [ITK-dev] ITK Software Guide In-Reply-To: <126188563.522813.1522173581831@mail.yahoo.com> References: <1920304591.517234.1522172553991.ref@mail.yahoo.com> <1920304591.517234.1522172553991@mail.yahoo.com> <126188563.522813.1522173581831@mail.yahoo.com> Message-ID: Hi Celina, I only see "Voronoi region" mentioned once here: https://github.com/InsightSoftwareConsortium/ITKSoftwareGuide/blob/7eb1f6dda1e5bfe57938f53584113ee771b298a7/SoftwareGuide/Latex/DesignAndFunctionality/HybridSegmentationMethods.tex Perhaps we just replace "Voronoi region" with "region"? Other improvements to make the language more accurate / precise are welcome. Thanks, Matt On Tue, Mar 27, 2018 at 1:59 PM, Celina Imielinska < celina_imielinska at yahoo.com> wrote: > > Hello Matt, > > thank you for your email... > > I agree it - but this one of the fundamendat geometric constructs used in > the Guide - that is just ill-named... > > How can we name it differently.... definitely, not as Voronoi region, nor > Delaunay region (completely wrong) > > -let us discuss, > > Best, > > Celina > ------------------------------ > *From:* Matt McCormick > *To:* Celina Imielinska > *Cc:* Stephen Aylward ; Bradley Lowekamp < > blowekamp at mail.nih.gov>; Insight Developers ; > Luis Ibanez > *Sent:* Tuesday, March 27, 2018 1:48 PM > *Subject:* Re: [ITK-dev] ITK Software Guide > > Hi Celina, > > Improvements to the Software Guide are welcome. Please see the README here > on how to contribute: > > https://github.com/InsightSoftwareConsortium/ITKSoftwareGuide > > Thanks, > Matt > > On Tue, Mar 27, 2018 at 1:42 PM, Celina Imielinska via Insight-developers > wrote: > > > Dear All > > (I have emailed separately Bill Schroeder at Kitware) > > I am very happy that ITK Toolkit has been thriving over so many years. > Kitware has done amazing job to maintain it and to expand it. > > Still, I am trying to contact the main co-authors of the currect ITK > Software Guide. > > I am writing about the usage of "Voronoi Region" terminology in the recent > editions of the ITK Software guide - that is very odd and not in agreement > with how Voronoi Diagram, that is one of the fundamental geometric > structures, is defined: > https://www.cs.ucsb.edu/~suri/ cs235/Voronoi.pdf > > > > Could you please email me - I would like to suggest that if we want to > use as "geometrical concepts associated with the ITK image" "Voronoi > region" in a form what I consider a degenerative representation of it - > then maybe it would be wise to name it differently. Not to mention the > usage of another oddity: Delaunay Region - what is it? Voronoi Diagram and > its dual, Delaunay Triangulation are classic geometric constructs that > require that the points, in the Voronoi diagram, the Voronoi points, > satisfy: > > "Non-degeneracy Condition: Assume no 4 cocircular points, and no 3 > collinear." > > This is violated in the construct included in the Guide and referred to as > Voronoi Region and Delaunay Region. > > I don't mind that the guide is not including any more my original hybrid > segmentation contribution that included Voronoi Diagram classification > https://core.ac.uk/download/ pdf/27299860.pdf > > I woudl like to ask you to discuss what can be done with possibly > correctingthe odd terminology, > > looking forward to hear from > > Best Regards, > > Celina Imielinska > > Celina Imielinska, PhD > Principal > Vesalius Technologies LLC > Princeton NJ > celina_imielinska at yahoo.com > 609 240 4721 > > PS. old version http://www.sci.utah. edu/publications/ibanez03/ > ItkSoftwareGuide.pdf > > newest https://itk.org/ ItkSoftwareGuide.pdf > > > 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://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-developers > > > > > > -------------- 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://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-developers From matt.mccormick at kitware.com Tue Mar 27 14:45:34 2018 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 27 Mar 2018 14:45:34 -0400 Subject: [ITK] [ITK-dev] ITK Software Guide In-Reply-To: <1655047778.574482.1522174955911@mail.yahoo.com> References: <1920304591.517234.1522172553991.ref@mail.yahoo.com> <1920304591.517234.1522172553991@mail.yahoo.com> <126188563.522813.1522173581831@mail.yahoo.com> <1655047778.574482.1522174955911@mail.yahoo.com> Message-ID: Ah, I see now, Celina. Thanks for sharing the screenshots. How about removing the mention of Voronoi region and Delaunay region from that location in the text and changing the annotation in the text to "Pixel Centered Region" and "Pixel-Corner Centered Region"? - M On Tue, Mar 27, 2018 at 2:22 PM, Celina Imielinska < celina_imielinska at yahoo.com> wrote: > in the attached document > > page 41 > in section > 4.1.4 Defining Origin and Spacing > > > ------------------------------ > *From:* Matt McCormick > *To:* Celina Imielinska > *Cc:* Stephen Aylward ; Bradley Lowekamp < > blowekamp at mail.nih.gov>; Insight Developers ; > Luis Ibanez > *Sent:* Tuesday, March 27, 2018 2:09 PM > > *Subject:* Re: [ITK-dev] ITK Software Guide > > Hi Celina, > > I only see "Voronoi region" mentioned once here: > > https://github.com/InsightSoftwareConsortium/ITKSoftwareGuide/blob/ > 7eb1f6dda1e5bfe57938f53584113ee771b298a7/SoftwareGuide/ > Latex/DesignAndFunctionality/HybridSegmentationMethods.tex > > Perhaps we just replace "Voronoi region" with "region"? > > > Other improvements to make the language more accurate / precise are > welcome. > > > Thanks, > Matt > > > > On Tue, Mar 27, 2018 at 1:59 PM, Celina Imielinska < > celina_imielinska at yahoo.com> wrote: > > > Hello Matt, > > thank you for your email... > > I agree it - but this one of the fundamendat geometric constructs used in > the Guide - that is just ill-named... > > How can we name it differently.... definitely, not as Voronoi region, nor > Delaunay region (completely wrong) > > -let us discuss, > > Best, > > Celina > ------------------------------ > *From:* Matt McCormick > *To:* Celina Imielinska > *Cc:* Stephen Aylward ; Bradley Lowekamp < > blowekamp at mail.nih.gov>; Insight Developers ; > Luis Ibanez > *Sent:* Tuesday, March 27, 2018 1:48 PM > *Subject:* Re: [ITK-dev] ITK Software Guide > > Hi Celina, > > Improvements to the Software Guide are welcome. Please see the README here > on how to contribute: > > https://github.com/ InsightSoftwareConsortium/ ITKSoftwareGuide > > > Thanks, > Matt > > On Tue, Mar 27, 2018 at 1:42 PM, Celina Imielinska via Insight-developers > wrote: > > > Dear All > > (I have emailed separately Bill Schroeder at Kitware) > > I am very happy that ITK Toolkit has been thriving over so many years. > Kitware has done amazing job to maintain it and to expand it. > > Still, I am trying to contact the main co-authors of the currect ITK > Software Guide. > > I am writing about the usage of "Voronoi Region" terminology in the recent > editions of the ITK Software guide - that is very odd and not in agreement > with how Voronoi Diagram, that is one of the fundamental geometric > structures, is defined: > https://www.cs.ucsb.edu/~suri/ cs235/Voronoi.pdf > > > > Could you please email me - I would like to suggest that if we want to > use as "geometrical concepts associated with the ITK image" "Voronoi > region" in a form what I consider a degenerative representation of it - > then maybe it would be wise to name it differently. Not to mention the > usage of another oddity: Delaunay Region - what is it? Voronoi Diagram and > its dual, Delaunay Triangulation are classic geometric constructs that > require that the points, in the Voronoi diagram, the Voronoi points, > satisfy: > > "Non-degeneracy Condition: Assume no 4 cocircular points, and no 3 > collinear." > > This is violated in the construct included in the Guide and referred to as > Voronoi Region and Delaunay Region. > > I don't mind that the guide is not including any more my original hybrid > segmentation contribution that included Voronoi Diagram classification > https://core.ac.uk/download/ pdf/27299860.pdf > > I woudl like to ask you to discuss what can be done with possibly > correctingthe odd terminology, > > looking forward to hear from > > Best Regards, > > Celina Imielinska > > Celina Imielinska, PhD > Principal > Vesalius Technologies LLC > Princeton NJ > celina_imielinska at yahoo.com > 609 240 4721 > > PS. old version http://www.sci.utah. edu/publications/ibanez03/ > ItkSoftwareGuide.pdf > > newest https://itk.org/ ItkSoftwareGuide.pdf > > > 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://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-developers > > > > > > > > > -------------- 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://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-developers From blowekamp at mail.nih.gov Tue Mar 27 15:23:03 2018 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Tue, 27 Mar 2018 19:23:03 +0000 Subject: [ITK] [ANNOUNCE] SimpleITK 1.1.0 Release Message-ID: We are pleased to announce the SimpleITK 1.1 Release! ### Installing SimpleITK Complete instructions on getting started with SimpleITK including downloading binaries or building SimpleITK can be found on the SimpleITK Read the Docs web page (http://simpleitk.readthedocs.io/en/release/Documentation/docs/source/installation.html). - Python Binary Downloads - Python binary wheels are available for download. It is important to have the latest version of pip for correct wheel compatibility and installation. To install the latest SimpleITK package form PyPI: python -m pip install --upgrade pip python -m pip install SimpleITK - Many Conda packages have been upload to Anaconda Cloud on the `SimpleITK` channel. These can be installed with: conda install -c simpleitk simpleitk - A complete available set of compiled binaries, including select CSharp and Java distributions, along with source and data tar-balls are available on Source Forge (https://sourceforge.net/projects/simpleitk/files/SimpleITK/1.1.0/). ## Release Notes Improvements: - Enabled 4D Images for IO, ExtractImageFilter, and output of JoinSeriesImageFilter. - Enabled MINC IO by default. - New Filters: `ObjectnessMeasuresImageFiler` (Frangi's vesselness), `IterativeInverseDisplacementFieldImageFilter`, `UnsharpMaskImageFilter`, and `RoundImageFilter`. - Added LBFGS2 optimizer to ImageRegistrationMethod. - Improved Show search path for FIJI now includes home directories. - Improved ITK Modular awareness, including ImageIOs. - Superbuild update PCRE 8.40, SWIG 3.0.12, ITK 4.13. - Many bug fixes and a couple segmentation fault issues addressed. - The build system is better and more robust then ever! Many new improvements and features! - Migrating examples, miscellaneous documentation and Wiki to Read the Docs: http://simpleitk.readthedocs.io/en/master/ - Improved reading and writing of 64-bit integer images across platforms (except python 2.7 on Windows). - Added optional wrapping of the `CoherenceEnahancingDiffusionImageFilter` (not enabled in binary distributions). - Added and improved examples related to DICOM reading, writing and manipulating the meta-data dictionary. API Changes: - Added `ImageFileReader::ReadImageInformation`. - This adds support to read meta-data from any supported image file format with any dimension without reading the bulk pixel data. - Added `ImageReaderBase::GetRegisteredImageIOs` method to obtain list of loaded ITK ImageIO modules. - Added `Version::ITKModulesEnabled` method to obtain a list of ITK enabled modules when SimpleITK was built. - Added `BinaryImageToLabelMap::GetNumberOfObjects`. - Added optional MaskImage input to `ConnectedComponentImageFilter`. - Added `SignedMaurerDistanceMapImageFilter::BackgroundValue` paramater. - `WarpImageFilter` now uses named inputs. - Convolution filters use named inputs. - Added optional OrientedBoundingBox to `LabelShapeStatisticsImageFilter`. - Added missing features to `RelabelComponentImageFilter` including `SortByObjectSize` parameter and `NumberOfObjects`, `SizeOfObjectsInPhysicalUnits` measurements. - Added `LabelStatisticsImageFilter::GetRegion`. - Added MetaDataDictionaries to the `ImageSeriesReader`. Compatibility: - `DiscreteGaussianImageFilter`, `SmoothingRecursiveGaussianImageFilter` now optionally take a vector argument for variance and sigma respectfully. - In Python the procedural methods, `DiscreteGaussian` and `SmoothingRecursiveGaussian` may not work with named arguments due to limitation with SWIG and overloaded functions. - `N4BiasFiledCorrectionImageFilter` now only takes uint8 pixel types for mask image input. Enjoy! Bradley Lowekamp -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Tue Mar 27 17:23:30 2018 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 27 Mar 2018 17:23:30 -0400 Subject: [ITK] [ITK-dev] ITK Software Guide In-Reply-To: <798829727.610059.1522181974720@mail.yahoo.com> References: <798829727.610059.1522181974720.ref@mail.yahoo.com> <798829727.610059.1522181974720@mail.yahoo.com> Message-ID: Thank you for efforts to improve the work, Celina. The ITK Software Guide is a living document, and many students should continue to learn from the body of knowledge that Luis poured out many years ago. Here is a patch for the figure: https://github.com/InsightSoftwareConsortium/ITKSoftwareGuide/pull/65 and the text: http://review.source.kitware.com/#/c/23300/ Thanks, Matt On Tue, Mar 27, 2018 at 4:19 PM, Celina Imielinska < celina_imielinska at yahoo.com> wrote: > That would be appropriate > > Thank you! > -------------------------------------------- > On Tue, 3/27/18, Matt McCormick wrote: > > Subject: Re: [ITK-dev] ITK Software Guide > To: "Celina Imielinska" > Cc: "Stephen Aylward" , "Bradley Lowekamp" < > blowekamp at mail.nih.gov>, "Insight Developers" , > "Luis Ibanez" > Date: Tuesday, March 27, 2018, 2:45 PM > > Ah, I see > now, Celina. Thanks for sharing the screenshots. > How about removing the mention of > Voronoi region and Delaunay region from that location in the > text and changing the annotation in the text to "Pixel > Centered Region" and "Pixel-Corner Centered > Region"? > - > M > On Tue, Mar 27, 2018 at > 2:22 PM, Celina Imielinska > wrote: > in > the attached document > page > 41in > section4.1.4 > Defining Origin and Spacing > > > > From: Matt McCormick > > To: Celina Imielinska > > > Cc: Stephen Aylward > ; > Bradley Lowekamp ; > Insight Developers ; > Luis Ibanez > Sent: Tuesday, March > 27, 2018 2:09 PM > Subject: Re: [ITK-dev] > ITK Software Guide > > > Hi Celina, > I only > see "Voronoi region" mentioned once > here: > https://github.com/ > InsightSoftwareConsortium/ ITKSoftwareGuide/blob/ > 7eb1f6dda1e5bfe57938f53584113e e771b298a7/SoftwareGuide/ > Latex/DesignAndFunctionality/ > HybridSegmentationMethods.tex > Perhaps we just replace > "Voronoi region" with > "region"? > > Other > improvements to make the language more accurate / precise > are welcome. > > Thanks,Matt > > > On > Tue, Mar 27, 2018 at 1:59 PM, Celina Imielinska < > celina_imielinska at yahoo.com> > wrote: > > Hello Matt, > thank > you for your email... > I > agree it - but this one of the fundamendat geometric > constructs used in the Guide - that is just > ill-named... > How > can we name it differently.... definitely, not as Voronoi > region, nor Delaunay region (completely wrong) > -let > us discuss, > Best, > Celina > From: Matt > McCormick > To: Celina Imielinska > > > Cc: Stephen Aylward > ; > Bradley Lowekamp ; > Insight Developers ; > Luis Ibanez > Sent: Tuesday, March > 27, 2018 1:48 PM > Subject: Re: [ITK-dev] > ITK Software Guide > > > > Hi Celina, > Improvements to the Software Guide > are welcome. Please see the README here on how to > contribute: > https://github.com/ > InsightSoftwareConsortium/ > ITKSoftwareGuide > Thanks,Matt > On > Tue, Mar 27, 2018 at 1:42 PM, Celina Imielinska via > Insight-developers > wrote: > > Dear > All > (I > have emailed separately Bill Schroeder at Kitware) > I > am very happy that ITK Toolkit has been thriving over so > many years. Kitware has done amazing job to maintain it and > to expand it. > Still, > I am trying to contact the main co-authors of the currect > ITK Software Guide. > I > am writing about the usage of "Voronoi Region" > terminology in the recent editions of the ITK Software guide > - that is very odd and not in agreement with how Voronoi > Diagram, that is one of the fundamental geometric > structures, is defined:https://www.cs.ucsb.edu/~suri/ > cs235/Voronoi.pdf > > Could > you please email me - I would like to suggest that if we > want to use as "geometrical concepts associated with > the ITK image" "Voronoi region" in a form > what I consider a degenerative representation of it - then > maybe it would be wise to name it differently. Not to > mention the usage of another oddity: Delaunay Region - > what is it? Voronoi Diagram and its dual, Delaunay > Triangulation are classic geometric constructs that require > that the points, in the Voronoi diagram, the Voronoi points, > satisfy: > "Non-degeneracy > Condition: Assume no 4 cocircular points, and no 3 > collinear." > This > is violated in the construct included in the Guide and > referred to as Voronoi Region and Delaunay Region. > I > don't mind that the guide is not including any more my > original hybrid segmentation contribution that included > Voronoi Diagram classification https://core.ac.uk/download/ > pdf/27299860.pdfI > woudl like to ask you to discuss what can be done with > possibly correctingthe odd terminology, > looking > forward to hear from > Best > Regards, > Celina > Imielinska > Celina > Imielinska, PhDPrincipalVesalius > Technologies LLCPrinceton > NJcelina_imielinska at yahoo.com609 240 4721 > PS. > old version http://www.sci.utah. > edu/publications/ibanez03/ > ItkSoftwareGuide.pdf > newest https://itk.org/ > ItkSoftwareGuide.pdf > 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://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-developers > > > > > > > > > > > > > -------------- 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://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-developers From matt.mccormick at kitware.com Wed Mar 28 10:18:01 2018 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 28 Mar 2018 10:18:01 -0400 Subject: [ITK] [ITK-dev] ITK Software Guide In-Reply-To: <1098703884.244169.1522244128697@mail.yahoo.com> References: <798829727.610059.1522181974720.ref@mail.yahoo.com> <798829727.610059.1522181974720@mail.yahoo.com> <1523366140.262107.1522243260582@mail.yahoo.com> <1098703884.244169.1522244128697@mail.yahoo.com> Message-ID: Hi Celina, The patch for this is here: http://review.source.kitware.com/#/c/23300/ - M On Wed, Mar 28, 2018 at 9:35 AM, Celina Imielinska < celina_imielinska at yahoo.com> wrote: > Matt, > > do you plan to correct the actual document? > > https://itk.org/ItkSoftwareGuide.pdf > > In the text, in the section 4.1.4, pages 41 and 42 : > "A pixel is considered to be the rectangular region surrounding the pixel > center holding the data value. This can be viewed as the *Voronoi region > of the image grid,* as illustrated in the right side of the figure. > Linear interpolation of image values is performed inside the* Delaunay > region whose corners are pixel centers*." > > these statements "Voronoi region of the image grid" and "Delaunay region > whose corners are pixed centers" - should go. > > the image 4.1 "Geometrical concepts associated with the ITK image", > should be redone too. In the image "Linear Interpolation Region Delaunay > Region" and "Pixel Coverage Voronoi Region" must be replaced, > > This document is used and shared by many and should not include confusing > terminology. > > Thanks again, > > Celina > ------------------------------ > *From:* Celina Imielinska > *To:* Matt McCormick > *Sent:* Wednesday, March 28, 2018 9:21 AM > > *Subject:* Re: [ITK-dev] ITK Software Guide > > Matt, > > thank you for the correction, > > Celina > > ------------------------------ > *From:* Matt McCormick > *To:* Celina Imielinska > *Cc:* Stephen Aylward ; Bradley Lowekamp < > blowekamp at mail.nih.gov>; Insight Developers ; > Luis Ibanez > *Sent:* Tuesday, March 27, 2018 5:23 PM > *Subject:* Re: [ITK-dev] ITK Software Guide > > Thank you for efforts to improve the work, Celina. The ITK Software Guide > is a living document, and many students should continue to learn from the > body of knowledge that Luis poured out many years ago. > > > Here is a patch for the figure: > > https://github.com/InsightSoftwareConsortium/ITKSoftwareGuide/pull/65 > > and the text: > > http://review.source.kitware.com/#/c/23300/ > > > Thanks, > Matt > > On Tue, Mar 27, 2018 at 4:19 PM, Celina Imielinska < > celina_imielinska at yahoo.com> wrote: > > That would be appropriate > > Thank you! > ------------------------------ -------------- > On Tue, 3/27/18, Matt McCormick wrote: > > Subject: Re: [ITK-dev] ITK Software Guide > To: "Celina Imielinska" > Cc: "Stephen Aylward" , "Bradley Lowekamp" < > blowekamp at mail.nih.gov>, "Insight Developers" , > "Luis Ibanez" > Date: Tuesday, March 27, 2018, 2:45 PM > > Ah, I see > now, Celina. Thanks for sharing the screenshots. > How about removing the mention of > Voronoi region and Delaunay region from that location in the > text and changing the annotation in the text to "Pixel > Centered Region" and "Pixel-Corner Centered > Region"? > - > M > On Tue, Mar 27, 2018 at > 2:22 PM, Celina Imielinska > wrote: > in > the attached document > page > 41in > section4.1.4 > Defining Origin and Spacing > > > > From: Matt McCormick > > To: Celina Imielinska > > > Cc: Stephen Aylward > ; > Bradley Lowekamp ; > Insight Developers ; > Luis Ibanez > Sent: Tuesday, March > 27, 2018 2:09 PM > Subject: Re: [ITK-dev] > ITK Software Guide > > > Hi Celina, > I only > see "Voronoi region" mentioned once > here: > https://github.com/ > InsightSoftwareConsortium/ ITKSoftwareGuide/blob/ > 7eb1f6dda1e5bfe57938f53584113e e771b298a7/SoftwareGuide/ > Latex/DesignAndFunctionality/ > HybridSegmentationMethods.tex > Perhaps we just replace > "Voronoi region" with > "region"? > > Other > improvements to make the language more accurate / precise > are welcome. > > Thanks,Matt > > > On > Tue, Mar 27, 2018 at 1:59 PM, Celina Imielinska < > celina_imielinska at yahoo.com> > wrote: > > Hello Matt, > thank > you for your email... > I > agree it - but this one of the fundamendat geometric > constructs used in the Guide - that is just > ill-named... > How > can we name it differently.... definitely, not as Voronoi > region, nor Delaunay region (completely wrong) > -let > us discuss, > Best, > Celina > From: Matt > McCormick > To: Celina Imielinska > > > Cc: Stephen Aylward > ; > Bradley Lowekamp ; > Insight Developers ; > Luis Ibanez > Sent: Tuesday, March > 27, 2018 1:48 PM > Subject: Re: [ITK-dev] > ITK Software Guide > > > > Hi Celina, > Improvements to the Software Guide > are welcome. Please see the README here on how to > contribute: > https://github.com/ > InsightSoftwareConsortium/ > ITKSoftwareGuide > Thanks,Matt > On > Tue, Mar 27, 2018 at 1:42 PM, Celina Imielinska via > Insight-developers > wrote: > > Dear > All > (I > have emailed separately Bill Schroeder at Kitware) > I > am very happy that ITK Toolkit has been thriving over so > many years. Kitware has done amazing job to maintain it and > to expand it. > Still, > I am trying to contact the main co-authors of the currect > ITK Software Guide. > I > am writing about the usage of "Voronoi Region" > terminology in the recent editions of the ITK Software guide > - that is very odd and not in agreement with how Voronoi > Diagram, that is one of the fundamental geometric > structures, is defined:https://www.cs.ucsb. edu/~suri/ > > cs235/Voronoi.pdf > > Could > you please email me - I would like to suggest that if we > want to use as "geometrical concepts associated with > the ITK image" "Voronoi region" in a form > what I consider a degenerative representation of it - then > maybe it would be wise to name it differently. Not to > mention the usage of another oddity: Delaunay Region - > what is it? Voronoi Diagram and its dual, Delaunay > Triangulation are classic geometric constructs that require > that the points, in the Voronoi diagram, the Voronoi points, > satisfy: > "Non-degeneracy > Condition: Assume no 4 cocircular points, and no 3 > collinear." > This > is violated in the construct included in the Guide and > referred to as Voronoi Region and Delaunay Region. > I > don't mind that the guide is not including any more my > original hybrid segmentation contribution that included > Voronoi Diagram classification https://core. ac.uk/download/ > > pdf/27299860.pdfI > woudl like to ask you to discuss what can be done with > possibly correctingthe odd terminology, > looking > forward to hear from > Best > Regards, > Celina > Imielinska > Celina > Imielinska, PhDPrincipalVesalius > Technologies LLCPrinceton > NJcelina_imielinska at yahoo. com609 240 4721 > PS. > old version http://www.sci.utah. > edu/publications/ibanez03/ > ItkSoftwareGuide.pdf > newest https://itk.org/ > ItkSoftwareGuide.pdf > 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://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-developers > > > > > > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... 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