From m.clarkson at ucl.ac.uk Fri Jun 13 04:49:46 2014 From: m.clarkson at ucl.ac.uk (Clarkson, Matt) Date: Fri, 13 Jun 2014 08:49:46 +0000 Subject: [Ctk-developers] Command Line Modules Message-ID: <865FD103-FB81-4C44-91E8-430E6A5C5458@live.ucl.ac.uk> Hi there, please can people clarify something. In the Slicer Execution Model wiki page [1], it says that the list of file extensions should be a comma separated list of extensions, which I read to mean ?no asterisks?. So, something like ?nii,nii.gz,mha? and NOT ?*.nii,*.nii.gz,*.mha?. Also, the CTK XSD file seems to agree with that: Can people please reply to me to confirm if they are in agreement/disagreement. And even better? please can people test their respective applications, and confirm if this is all working as it should be? I think people need to be careful to check both input and output. In many cases, the input side may well be masked by the application. For example, if the application loads an image into memory, and an ?input? combo box simply lists the images currently available memory, then you wont be able to check whether a file open dialog box is actually doing as it should be. Thanks Matt [1] http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation [2] https://github.com/commontk/CTK/blob/master/Libs/CommandLineModules/Core/Resources/ctkCmdLineModule.xsd#L431 -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.zelzer at dkfz-heidelberg.de Tue Jun 17 15:50:31 2014 From: s.zelzer at dkfz-heidelberg.de (Sascha Zelzer) Date: Tue, 17 Jun 2014 21:50:31 +0200 Subject: [Ctk-developers] Command Line Modules In-Reply-To: <865FD103-FB81-4C44-91E8-430E6A5C5458@live.ucl.ac.uk> References: <865FD103-FB81-4C44-91E8-430E6A5C5458@live.ucl.ac.uk> Message-ID: <53A09C07.2060305@dkfz-heidelberg.de> Hi, I was curiously waiting for a reply myself. My interpretation of the extensions list for files is the same as Matts, but if people use it differently or just "post-process" the file extensions list to fit their expectations, this would be good to know. Thanks, Sascha On 06/13/2014 10:49 AM, Clarkson, Matt wrote: > Hi there, > > please can people clarify something. In the Slicer Execution Model > wiki page [1], it says that the list of file extensions should be a > comma separated list of extensions, which I read to mean ?no > asterisks?. So, something like ?nii,nii.gz,mha? and NOT > ?*.nii,*.nii.gz,*.mha?. Also, the CTK XSD file seems to agree with that: > > Can people please reply to me to confirm if they are in > agreement/disagreement. > And even better? please can people test their respective applications, > and confirm if this is all working as it should be? > > I think people need to be careful to check both input and output. In > many cases, the input side may well be masked by the application. For > example, if the application loads an image into memory, and an ?input? > combo box simply lists the images currently available memory, then you > wont be able to check whether a file open dialog box is actually doing > as it should be. > > Thanks > > Matt > > [1] > http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation > [2] > https://github.com/commontk/CTK/blob/master/Libs/CommandLineModules/Core/Resources/ctkCmdLineModule.xsd#L431 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From florian.vichot at inria.fr Thu Jun 19 13:56:50 2014 From: florian.vichot at inria.fr (Florian Vichot) Date: Thu, 19 Jun 2014 19:56:50 +0200 (CEST) Subject: [Ctk-developers] Command Line Modules In-Reply-To: <53A09C07.2060305@dkfz-heidelberg.de> References: <865FD103-FB81-4C44-91E8-430E6A5C5458@live.ucl.ac.uk> <53A09C07.2060305@dkfz-heidelberg.de> Message-ID: <1866049113.2959267.1403200610265.JavaMail.zimbra@inria.fr> Hey all, I do some post-processing, I strip the '*' from the extension list, but keep the leading dot, as that's the way we format supported extensions in the read/writer plugins in medInria. Do you have examples in the wild of CLIs that output XML without the asterisk ? All the ones I have here (niftyreg tools, the CTK test binaries) have asterisks in their extension lists. Florian ----- Mail original ----- > De: "Sascha Zelzer" > ?: "Matt Clarkson" , ctk-developers at commontk.org > Envoy?: Mardi 17 Juin 2014 21:50:31 > Objet: Re: [Ctk-developers] Command Line Modules > Hi, > I was curiously waiting for a reply myself. My interpretation of the > extensions list for files is the same as Matts, but if people use it > differently or just "post-process" the file extensions list to fit their > expectations, this would be good to know. > Thanks, > Sascha > On 06/13/2014 10:49 AM, Clarkson, Matt wrote: > > Hi there, > > > please can people clarify something. In the Slicer Execution Model wiki > > page > > [1], it says that the list of file extensions should be a comma separated > > list of extensions, which I read to mean ?no asterisks?. So, something like > > ?nii,nii.gz,mha? and NOT ?*.nii,*.nii.gz,*.mha?. Also, the CTK XSD file > > seems to agree with that: > > > Can people please reply to me to confirm if they are in > > agreement/disagreement. > > > And even better? please can people test their respective applications, and > > confirm if this is all working as it should be? > > > I think people need to be careful to check both input and output. In many > > cases, the input side may well be masked by the application. For example, > > if > > the application loads an image into memory, and an ?input? combo box simply > > lists the images currently available memory, then you wont be able to check > > whether a file open dialog box is actually doing as it should be. > > > Thanks > > > Matt > > > [1] > > http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation > > > [2] > > https://github.com/commontk/CTK/blob/master/Libs/CommandLineModules/Core/Resources/ctkCmdLineModule.xsd#L431 > > _______________________________________________ > Ctk-developers mailing list > Ctk-developers at public.kitware.com > http://public.kitware.com/mailman/listinfo/ctk-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.clarkson at ucl.ac.uk Thu Jun 19 14:48:19 2014 From: m.clarkson at ucl.ac.uk (Clarkson, Matt) Date: Thu, 19 Jun 2014 18:48:19 +0000 Subject: [Ctk-developers] Command Line Modules In-Reply-To: <1866049113.2959267.1403200610265.JavaMail.zimbra@inria.fr> References: <865FD103-FB81-4C44-91E8-430E6A5C5458@live.ucl.ac.uk> <53A09C07.2060305@dkfz-heidelberg.de> <1866049113.2959267.1403200610265.JavaMail.zimbra@inria.fr> Message-ID: <1FD046D4-6ABB-4B16-AEF4-2461FAA9589C@live.ucl.ac.uk> Hey Florian, yeap ? that?s why I ask. Later versions of NiftyReg have now dropped the *. http://sourceforge.net/p/niftyreg/git/ci/master/tree/reg-apps/reg_aladin.h#l29 i believe this is because CTK .xsd says its without the *. We don?t mind what it is, we just need to all agree :-) M On 19 Jun 2014, at 18:56, Florian Vichot > wrote: Hey all, I do some post-processing, I strip the '*' from the extension list, but keep the leading dot, as that's the way we format supported extensions in the read/writer plugins in medInria. Do you have examples in the wild of CLIs that output XML without the asterisk ? All the ones I have here (niftyreg tools, the CTK test binaries) have asterisks in their extension lists. Florian ________________________________ De: "Sascha Zelzer" > ?: "Matt Clarkson" >, ctk-developers at commontk.org Envoy?: Mardi 17 Juin 2014 21:50:31 Objet: Re: [Ctk-developers] Command Line Modules Hi, I was curiously waiting for a reply myself. My interpretation of the extensions list for files is the same as Matts, but if people use it differently or just "post-process" the file extensions list to fit their expectations, this would be good to know. Thanks, Sascha On 06/13/2014 10:49 AM, Clarkson, Matt wrote: Hi there, please can people clarify something. In the Slicer Execution Model wiki page [1], it says that the list of file extensions should be a comma separated list of extensions, which I read to mean ?no asterisks?. So, something like ?nii,nii.gz,mha? and NOT ?*.nii,*.nii.gz,*.mha?. Also, the CTK XSD file seems to agree with that: Can people please reply to me to confirm if they are in agreement/disagreement. And even better? please can people test their respective applications, and confirm if this is all working as it should be? I think people need to be careful to check both input and output. In many cases, the input side may well be masked by the application. For example, if the application loads an image into memory, and an ?input? combo box simply lists the images currently available memory, then you wont be able to check whether a file open dialog box is actually doing as it should be. Thanks Matt [1] http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation [2] https://github.com/commontk/CTK/blob/master/Libs/CommandLineModules/Core/Resources/ctkCmdLineModule.xsd#L431 _______________________________________________ Ctk-developers mailing list Ctk-developers at public.kitware.com http://public.kitware.com/mailman/listinfo/ctk-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: From pieper at isomics.com Mon Jun 23 09:57:47 2014 From: pieper at isomics.com (Steve Pieper) Date: Mon, 23 Jun 2014 09:57:47 -0400 Subject: [Ctk-developers] summer project week and dicom breakout Message-ID: Hi CTKers - As some of you know this is summer project week at MIT and there is a lot going on that people may be interested in looking over [1]. In particular I wanted to draw attention to the 1.5 hour DICOM related breakout session [2]. We'll be setting up a google hangout so if anyone wants to participate remotely in the session let me know. -Steve [1] http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week [2] http://www.na-mic.org/Wiki/index.php/2014_Project_Week_Breakout_Session:_DICOM#Remote_participation -------------- next part -------------- An HTML attachment was scrubbed... URL: From pieper at isomics.com Sat Jun 28 12:43:16 2014 From: pieper at isomics.com (Steve Pieper) Date: Sat, 28 Jun 2014 12:43:16 -0400 Subject: [Ctk-developers] Fwd: Call 4 a Demo In-Reply-To: <95D64F46-C862-4793-98D6-53C0BD96B263@ee.bgu.ac.il> References: <95D64F46-C862-4793-98D6-53C0BD96B263@ee.bgu.ac.il> Message-ID: ---------- Forwarded message ---------- From: Tammy R. Raviv Date: Thu, Jun 26, 2014 at 7:51 AM Subject: Call 4 a Demo To: steve Pieper , yi Gao , Bjoern Menze Hi all, Please find below a call for a demo Please feel free to distribute. Thanks Tammy IMIC workshop ? a call for Demos We would like to invite you to actively participate at the Interactive Medical Image Computing (IMIC) Workshop by giving a live demo of your work. IMIC is to be held in Boston, on Sunday September 14, in conjunction with MICCAI 2014. We received many excellent paper submissions and plan to send notifications of acceptance for the oral and the demo sessions soon. While the deadline for manuscript submission to the IMIC has passed, there is still an opportunity to take part at the workshop and present your work in demo form. The IMIC workshop addresses the topic of human interaction with algorithms for initialization, steering, quality control, and visualization for problem domains such as segmentation and registration, object detection and tracking. The workshop format encourages hands-on demonstrations to stimulate interaction between developers and the user community of clinicians, neuroscientists, and biologists. Our focus is on original methods and elegant implementations that establish a human-machine dialog. Evaluation will be based on productivity, accuracy, simplicity, and overall user experience. Attendees are encouraged to bring challenging real-world datasets and allow active experimentation with various tools on different data. In this call for participation in the demo session of the workshop we ask for 300 words abstract along with a demo or a link to a toolbox. Submissions will be handled in an ongoing basis. We will send an acceptance notification to the demo session within a week of the submission. The latest date to submit a demo is August 15 but please note that we may reach the number of demos we can accommodate earlier. More details can be found in: http://interactivemedical.org/imic2014/ We look forward to seeing you at the IMIC The IMIC Organizers Steve Pieper Yi Gao Bjoern Menze Tammy Riklin Raviv -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.clarkson at ucl.ac.uk Fri Jun 13 04:49:46 2014 From: m.clarkson at ucl.ac.uk (Clarkson, Matt) Date: Fri, 13 Jun 2014 08:49:46 +0000 Subject: [Ctk-developers] Command Line Modules Message-ID: <865FD103-FB81-4C44-91E8-430E6A5C5458@live.ucl.ac.uk> Hi there, please can people clarify something. In the Slicer Execution Model wiki page [1], it says that the list of file extensions should be a comma separated list of extensions, which I read to mean ?no asterisks?. So, something like ?nii,nii.gz,mha? and NOT ?*.nii,*.nii.gz,*.mha?. Also, the CTK XSD file seems to agree with that: Can people please reply to me to confirm if they are in agreement/disagreement. And even better? please can people test their respective applications, and confirm if this is all working as it should be? I think people need to be careful to check both input and output. In many cases, the input side may well be masked by the application. For example, if the application loads an image into memory, and an ?input? combo box simply lists the images currently available memory, then you wont be able to check whether a file open dialog box is actually doing as it should be. Thanks Matt [1] http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation [2] https://github.com/commontk/CTK/blob/master/Libs/CommandLineModules/Core/Resources/ctkCmdLineModule.xsd#L431 -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.zelzer at dkfz-heidelberg.de Tue Jun 17 15:50:31 2014 From: s.zelzer at dkfz-heidelberg.de (Sascha Zelzer) Date: Tue, 17 Jun 2014 21:50:31 +0200 Subject: [Ctk-developers] Command Line Modules In-Reply-To: <865FD103-FB81-4C44-91E8-430E6A5C5458@live.ucl.ac.uk> References: <865FD103-FB81-4C44-91E8-430E6A5C5458@live.ucl.ac.uk> Message-ID: <53A09C07.2060305@dkfz-heidelberg.de> Hi, I was curiously waiting for a reply myself. My interpretation of the extensions list for files is the same as Matts, but if people use it differently or just "post-process" the file extensions list to fit their expectations, this would be good to know. Thanks, Sascha On 06/13/2014 10:49 AM, Clarkson, Matt wrote: > Hi there, > > please can people clarify something. In the Slicer Execution Model > wiki page [1], it says that the list of file extensions should be a > comma separated list of extensions, which I read to mean ?no > asterisks?. So, something like ?nii,nii.gz,mha? and NOT > ?*.nii,*.nii.gz,*.mha?. Also, the CTK XSD file seems to agree with that: > > Can people please reply to me to confirm if they are in > agreement/disagreement. > And even better? please can people test their respective applications, > and confirm if this is all working as it should be? > > I think people need to be careful to check both input and output. In > many cases, the input side may well be masked by the application. For > example, if the application loads an image into memory, and an ?input? > combo box simply lists the images currently available memory, then you > wont be able to check whether a file open dialog box is actually doing > as it should be. > > Thanks > > Matt > > [1] > http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation > [2] > https://github.com/commontk/CTK/blob/master/Libs/CommandLineModules/Core/Resources/ctkCmdLineModule.xsd#L431 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From florian.vichot at inria.fr Thu Jun 19 13:56:50 2014 From: florian.vichot at inria.fr (Florian Vichot) Date: Thu, 19 Jun 2014 19:56:50 +0200 (CEST) Subject: [Ctk-developers] Command Line Modules In-Reply-To: <53A09C07.2060305@dkfz-heidelberg.de> References: <865FD103-FB81-4C44-91E8-430E6A5C5458@live.ucl.ac.uk> <53A09C07.2060305@dkfz-heidelberg.de> Message-ID: <1866049113.2959267.1403200610265.JavaMail.zimbra@inria.fr> Hey all, I do some post-processing, I strip the '*' from the extension list, but keep the leading dot, as that's the way we format supported extensions in the read/writer plugins in medInria. Do you have examples in the wild of CLIs that output XML without the asterisk ? All the ones I have here (niftyreg tools, the CTK test binaries) have asterisks in their extension lists. Florian ----- Mail original ----- > De: "Sascha Zelzer" > ?: "Matt Clarkson" , ctk-developers at commontk.org > Envoy?: Mardi 17 Juin 2014 21:50:31 > Objet: Re: [Ctk-developers] Command Line Modules > Hi, > I was curiously waiting for a reply myself. My interpretation of the > extensions list for files is the same as Matts, but if people use it > differently or just "post-process" the file extensions list to fit their > expectations, this would be good to know. > Thanks, > Sascha > On 06/13/2014 10:49 AM, Clarkson, Matt wrote: > > Hi there, > > > please can people clarify something. In the Slicer Execution Model wiki > > page > > [1], it says that the list of file extensions should be a comma separated > > list of extensions, which I read to mean ?no asterisks?. So, something like > > ?nii,nii.gz,mha? and NOT ?*.nii,*.nii.gz,*.mha?. Also, the CTK XSD file > > seems to agree with that: > > > Can people please reply to me to confirm if they are in > > agreement/disagreement. > > > And even better? please can people test their respective applications, and > > confirm if this is all working as it should be? > > > I think people need to be careful to check both input and output. In many > > cases, the input side may well be masked by the application. For example, > > if > > the application loads an image into memory, and an ?input? combo box simply > > lists the images currently available memory, then you wont be able to check > > whether a file open dialog box is actually doing as it should be. > > > Thanks > > > Matt > > > [1] > > http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation > > > [2] > > https://github.com/commontk/CTK/blob/master/Libs/CommandLineModules/Core/Resources/ctkCmdLineModule.xsd#L431 > > _______________________________________________ > Ctk-developers mailing list > Ctk-developers at public.kitware.com > http://public.kitware.com/mailman/listinfo/ctk-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.clarkson at ucl.ac.uk Thu Jun 19 14:48:19 2014 From: m.clarkson at ucl.ac.uk (Clarkson, Matt) Date: Thu, 19 Jun 2014 18:48:19 +0000 Subject: [Ctk-developers] Command Line Modules In-Reply-To: <1866049113.2959267.1403200610265.JavaMail.zimbra@inria.fr> References: <865FD103-FB81-4C44-91E8-430E6A5C5458@live.ucl.ac.uk> <53A09C07.2060305@dkfz-heidelberg.de> <1866049113.2959267.1403200610265.JavaMail.zimbra@inria.fr> Message-ID: <1FD046D4-6ABB-4B16-AEF4-2461FAA9589C@live.ucl.ac.uk> Hey Florian, yeap ? that?s why I ask. Later versions of NiftyReg have now dropped the *. http://sourceforge.net/p/niftyreg/git/ci/master/tree/reg-apps/reg_aladin.h#l29 i believe this is because CTK .xsd says its without the *. We don?t mind what it is, we just need to all agree :-) M On 19 Jun 2014, at 18:56, Florian Vichot > wrote: Hey all, I do some post-processing, I strip the '*' from the extension list, but keep the leading dot, as that's the way we format supported extensions in the read/writer plugins in medInria. Do you have examples in the wild of CLIs that output XML without the asterisk ? All the ones I have here (niftyreg tools, the CTK test binaries) have asterisks in their extension lists. Florian ________________________________ De: "Sascha Zelzer" > ?: "Matt Clarkson" >, ctk-developers at commontk.org Envoy?: Mardi 17 Juin 2014 21:50:31 Objet: Re: [Ctk-developers] Command Line Modules Hi, I was curiously waiting for a reply myself. My interpretation of the extensions list for files is the same as Matts, but if people use it differently or just "post-process" the file extensions list to fit their expectations, this would be good to know. Thanks, Sascha On 06/13/2014 10:49 AM, Clarkson, Matt wrote: Hi there, please can people clarify something. In the Slicer Execution Model wiki page [1], it says that the list of file extensions should be a comma separated list of extensions, which I read to mean ?no asterisks?. So, something like ?nii,nii.gz,mha? and NOT ?*.nii,*.nii.gz,*.mha?. Also, the CTK XSD file seems to agree with that: Can people please reply to me to confirm if they are in agreement/disagreement. And even better? please can people test their respective applications, and confirm if this is all working as it should be? I think people need to be careful to check both input and output. In many cases, the input side may well be masked by the application. For example, if the application loads an image into memory, and an ?input? combo box simply lists the images currently available memory, then you wont be able to check whether a file open dialog box is actually doing as it should be. Thanks Matt [1] http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation [2] https://github.com/commontk/CTK/blob/master/Libs/CommandLineModules/Core/Resources/ctkCmdLineModule.xsd#L431 _______________________________________________ Ctk-developers mailing list Ctk-developers at public.kitware.com http://public.kitware.com/mailman/listinfo/ctk-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: From pieper at isomics.com Mon Jun 23 09:57:47 2014 From: pieper at isomics.com (Steve Pieper) Date: Mon, 23 Jun 2014 09:57:47 -0400 Subject: [Ctk-developers] summer project week and dicom breakout Message-ID: Hi CTKers - As some of you know this is summer project week at MIT and there is a lot going on that people may be interested in looking over [1]. In particular I wanted to draw attention to the 1.5 hour DICOM related breakout session [2]. We'll be setting up a google hangout so if anyone wants to participate remotely in the session let me know. -Steve [1] http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week [2] http://www.na-mic.org/Wiki/index.php/2014_Project_Week_Breakout_Session:_DICOM#Remote_participation -------------- next part -------------- An HTML attachment was scrubbed... URL: From pieper at isomics.com Sat Jun 28 12:43:16 2014 From: pieper at isomics.com (Steve Pieper) Date: Sat, 28 Jun 2014 12:43:16 -0400 Subject: [Ctk-developers] Fwd: Call 4 a Demo In-Reply-To: <95D64F46-C862-4793-98D6-53C0BD96B263@ee.bgu.ac.il> References: <95D64F46-C862-4793-98D6-53C0BD96B263@ee.bgu.ac.il> Message-ID: ---------- Forwarded message ---------- From: Tammy R. Raviv Date: Thu, Jun 26, 2014 at 7:51 AM Subject: Call 4 a Demo To: steve Pieper , yi Gao , Bjoern Menze Hi all, Please find below a call for a demo Please feel free to distribute. Thanks Tammy IMIC workshop ? a call for Demos We would like to invite you to actively participate at the Interactive Medical Image Computing (IMIC) Workshop by giving a live demo of your work. IMIC is to be held in Boston, on Sunday September 14, in conjunction with MICCAI 2014. We received many excellent paper submissions and plan to send notifications of acceptance for the oral and the demo sessions soon. While the deadline for manuscript submission to the IMIC has passed, there is still an opportunity to take part at the workshop and present your work in demo form. The IMIC workshop addresses the topic of human interaction with algorithms for initialization, steering, quality control, and visualization for problem domains such as segmentation and registration, object detection and tracking. The workshop format encourages hands-on demonstrations to stimulate interaction between developers and the user community of clinicians, neuroscientists, and biologists. Our focus is on original methods and elegant implementations that establish a human-machine dialog. Evaluation will be based on productivity, accuracy, simplicity, and overall user experience. Attendees are encouraged to bring challenging real-world datasets and allow active experimentation with various tools on different data. In this call for participation in the demo session of the workshop we ask for 300 words abstract along with a demo or a link to a toolbox. Submissions will be handled in an ongoing basis. We will send an acceptance notification to the demo session within a week of the submission. The latest date to submit a demo is August 15 but please note that we may reach the number of demos we can accommodate earlier. More details can be found in: http://interactivemedical.org/imic2014/ We look forward to seeing you at the IMIC The IMIC Organizers Steve Pieper Yi Gao Bjoern Menze Tammy Riklin Raviv -------------- next part -------------- An HTML attachment was scrubbed... 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