Dear Hu, maybe this is related to a mismatch between the build configuration (debug/release) specified via cmake and the one chosen in Visual Studio. Can you maybe send us the complete compile output?
If you face general issues such as build problems, the MITK mailing list ([email protected]<mailto:[email protected]>, https://lists.sourceforge.net/lists/listinfo/mitk-users) always is a great source for help. Peter From: Cheng, Hu [mailto:[email protected]] Sent: Donnerstag, 6. August 2015 05:15 To: Goch, Caspar Jonas; Neher, Peter; The Tractometer Team Subject: RE: generating MRI data from bundles Hi Peter and Caspar, Thank you very much for your help! I'm one more step closer. I built superbuild first and encountered a couple of errors showing "Debug assertion failed", I ignored the errors and the process was completed. In the end, I got the following message: Build: Build: 18 succeeded, 12 failed, 0 up-to-date, 2 skipped However, I don't see any executive files. How do I get the applications? I checked MITK-build folder, there are only three files (CMakeCache, CTestConfigSubProject, Project) and one folder (CMakeFiles). Regards, Hu From: Goch, Caspar Jonas [mailto:[email protected]] Sent: Wednesday, August 05, 2015 5:47 AM To: Neher, Peter; Cheng, Hu; The Tractometer Team Subject: AW: generating MRI data from bundles Hi Hu, just a quick addendum to Peters comments. CMake tests whether the used compiler support a couple of flags. That just influences whether those flags are then used. MITK builds fine without them, but it might be faster/more optimized if they are present. Do not worry about it unless there is an actual CMake error message. Building the MITK-superbuild.sln (on Windows, just run make in the superbuild directory on Linux) will build all toolkits as well as MITK itself. You only need to run CMake in and build the MITK-build directory if you want to change some settings from the default (such as switching on certain plugins which are, by default, disabled). Best, Caspar Von: Neher, Peter Gesendet: Mittwoch, 5. August 2015 11:34 An: Cheng, Hu; The Tractometer Team Cc: Goch, Caspar Jonas Betreff: RE: generating MRI data from bundles Dear Hu, the failed tests don't matter. Should work anyway. The MITK-Build folder is empty because you have to run the superbuild first. There should be a Visual Studio solution file in the top level binary folder (the folder that contains the MITK-Build folder). This project will build all the external toolkits (ITK, VTK, ...) needed by MITK. If this build was successful, run Cmake again on the MITK-Build folder. Then you will get the solution file to build MITK (don't forget to enable the options needed for the diffusion modules). What are the issues under Linux? Peter From: Cheng, Hu [mailto:[email protected]] Sent: Dienstag, 4. August 2015 16:42 To: Neher, Peter; The Tractometer Team Subject: RE: generating MRI data from bundles Dear Peter, We are trying to build MITK ourselves. However, this process has been unsuccessful on either Windows or Linux, very close on Windows though. The configure on CMake failed few tests but went through. Here are the message of the failed tests: Performing Test HAS_FLAG_-std=c11 Performing Test HAS_FLAG_-std=c11 - Failed Performing Test HAS_FLAG_-std=c0x Performing Test HAS_FLAG_-std=c0x - Failed Generated: C:/MITK-superbuild/Project.xml Performing Test HAS_FLAG_-Wl-rpath Performing Test HAS_FLAG_-Wl-rpath - Failed In the end, many files and new folders were generated, which was encouraging. However, the folder MITK-build was empty. I assume there should be a batch file that I can run according to the instruction. Now I don't know how to proceed. Do you have any clue? When do you expect the release of new version of Diffusion? Thank you very much for your help! Regards, Hu From: Peter Neher [mailto:[email protected]] Sent: Monday, July 20, 2015 11:49 AM To: Cheng, Hu; The Tractometer Team Subject: Re: generating MRI data from bundles You can find general build instructions for MITK here http://docs.mitk.org/nightly/BuildInstructionsPage.html Make sure to enable all cmake options necessary to build MITK Diffusion on the superbuild level (Boost, HDF5, Vigra) as well as later on the MITK build level (every option that contains "diffusion"). If you have any questions, don't hesitate to ask me and/or the MITK users mailing list ([email protected]<mailto:[email protected]>). Peter On 20.07.2015 17:44, Cheng, Hu wrote: Dear Peter, Thank you very much for the information. I look forward to the release of all data. We'll try to build MITK Diffusion in the meanwhile. Regards, Hu From: Peter Neher [mailto:[email protected]] Sent: Monday, July 20, 2015 11:22 AM To: The Tractometer Team; Cheng, Hu Subject: Re: generating MRI data from bundles Dear Hu, you are right, using only the fibers will not generate an image similar to the one we used for the challenge. We will publish all data that is needed for the simulation soon (volume fraction images for all 4 compartments, parameter file, ...). When using these files it is important to also use a new version of Fiberfox since we added some new features during the challenge preparation. This means that the currently released binary will probably not work as desired. You could either check out the current source code of MITK and build MITK Diffusion yourself, or you have to wait for the next release of MITK Diffusion. Peter On 20.07.2015 17:06, The Tractometer Team wrote: Dear Hu, thanks for your interest. I'm adding Peter Neher in CC to this email. He is responsible for Fiberfox and the generation of the data for the Challenge. He will be able to help you. If possible, can you keep this address CCed in the discussion? That way, we can add the final information to a FAQ if there is interest. Best regards. -- The Tractometer Team Le 2015-07-13 13:20, Cheng, Hu a écrit : Dear tractometer team, First thank you for your great contribution in the validation of tractography data. I downloaded the ground truth bundles and tried to simulate MRI signal from the bundles using fiberfox. I united all the bundles and ran the simulation. However, the outcome doesn't look like a MRI image. I guess I must miss something like the signal of gray matter. So how did you generate the MRI signal from all the bundles? Another question is it seems that the simulation doesn't take partial parallel imaging (e.g. GRAPPA) into account, would this something to consider in the future? Thank you very much. Hu Cheng, Ph.D., DABMP MRI Physicist, Imaging Research Facility Department of Psychological and Brain Sciences Adjunct Professor, Department of Physics Indiana University Bloomington, IN 47405 Tel. 812-856-2518 Fax. 812-855-4691
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