From majid.msadeghi at yahoo.com Fri Mar 2 10:20:45 2018 From: majid.msadeghi at yahoo.com (Majid M. Sadeghi) Date: Fri, 2 Mar 2018 15:20:45 +0000 (UTC) Subject: [ITK-users] object orientation detection References: <1903632477.9254637.1520004045990.ref@mail.yahoo.com> Message-ID: <1903632477.9254637.1520004045990@mail.yahoo.com> Dear All, I have a 3D object which is located in an arbitrary positionand orientation in the space. My goal is to roughly find the orientation of theobject. To achieve that, I think I need a descriptor of the object todefine it. For that descriptor I am thinking maybe a skeleton of the object willwork, since my object?s shape is a specific shape with certain twists andcorners. After having the descriptor I need to be able to find theorientation of the descriptor. And for this I am thinking I might be able touse certain relationships of points located on the skeleton, with each other orwith the origin of the space. So my questions are: 1. Is there a better method to do this? (Finding theorientation of an object) 2. Is there a method in VTK/ITK to extract the skeleton ofan object? 3. Is there any other descriptor available in VTK/ITK whichmight be helpful??Thanks. -------------- 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-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: 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-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/ 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-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/ 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-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: 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-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: 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-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: 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-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: 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-users] [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-users] 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-users] 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-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: 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-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: 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-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: 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-users] 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 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-users] [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: