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MIC-DKFZ / MITK-Diffusion

MITK Diffusion - Official part of the Medical Imaging Interaction Toolkit
http://mitk.org/wiki/MITK
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Can not load .trk file #2

Closed WilliamFCB closed 2 years ago

WilliamFCB commented 3 years ago

Hi Peter

I guess I do something terribly wrong when installing MITK

I downloaded MITK-v2021.02-linux-x86_64.tar.gz. Unpacked it, added the main and bin subdirectory to my $PATH in my .bashrc and successfully started the Workbench I can load nifty files, but when trying to a load a .trk tract file generated with TractSeg (trk_legacy format) I get the error "no reader available..."

Any, idea what I might have missed?

Many thanks in advance William

WilliamFCB commented 3 years ago

Just wait, can see it failed to load some libraries

WilliamFCB commented 3 years ago

I was missing libwrap.so.0

Still can't read .trk files When starting the workbench I get the following messages:

Using database: "/mrhome/wimb/.local/share/DKFZ/MITK Workbench_1780475261/plugins.db" Using database: "/mrhome/wimb/.local/share/DKFZ/MITK Workbench_1780475261/plugins.db" Using database: "/mrhome/wimb/.local/share/DKFZ/MITK Workbench_1780475261/plugins.db" Wed Apr 28 17:13:40 2021 Debug: org.commontk.eventadmin.LogLevel=2 in startOrUpdate, /home/ubuntu/jenkins-agent/MITK/Release/Ubuntu18.04/build/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:215 Wed Apr 28 17:13:40 2021 Debug: org.commontk.eventadmin.CacheSize=30 in startOrUpdate, /home/ubuntu/jenkins-agent/MITK/Release/Ubuntu18.04/build/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:217 Wed Apr 28 17:13:40 2021 Debug: org.commontk.eventadmin.ThreadPoolSize=20 in startOrUpdate, /home/ubuntu/jenkins-agent/MITK/Release/Ubuntu18.04/build/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:219 Wed Apr 28 17:13:40 2021 Debug: org.commontk.eventadmin.Timeout=5000 in startOrUpdate, /home/ubuntu/jenkins-agent/MITK/Release/Ubuntu18.04/build/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:221 Wed Apr 28 17:13:40 2021 Debug: org.commontk.eventadmin.RequireTopic=true in startOrUpdate, /home/ubuntu/jenkins-agent/MITK/Release/Ubuntu18.04/build/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:223 Wed Apr 28 17:13:40 2021 Debug: org.commontk.eventadmin.LogLevel=2 in startOrUpdate, /home/ubuntu/jenkins-agent/MITK/Release/Ubuntu18.04/build/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:215 Wed Apr 28 17:13:40 2021 Debug: org.commontk.eventadmin.CacheSize=30 in startOrUpdate, /home/ubuntu/jenkins-agent/MITK/Release/Ubuntu18.04/build/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:217 Wed Apr 28 17:13:40 2021 Debug: org.commontk.eventadmin.ThreadPoolSize=20 in startOrUpdate, /home/ubuntu/jenkins-agent/MITK/Release/Ubuntu18.04/build/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:219 Wed Apr 28 17:13:40 2021 Debug: org.commontk.eventadmin.Timeout=5000 in startOrUpdate, /home/ubuntu/jenkins-agent/MITK/Release/Ubuntu18.04/build/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:221 Wed Apr 28 17:13:40 2021 Debug: org.commontk.eventadmin.RequireTopic=true in startOrUpdate, /home/ubuntu/jenkins-agent/MITK/Release/Ubuntu18.04/build/ep/src/CTK/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:223 [Wed Apr 28 17:13:40 2021 0.939] Logfile: /mrhome/wimb/.local/share/DKFZ/MITK Workbench_1780475261/data/9/mitk-0.log [1.141] Set default layout [1.172] [BlueBerry] LOG: Warning: Detected recursive attempt by part org.mitk.views.datamanager to create itself (this is probably, but not necessarily, a bug) [2.420] [BlueBerry] BlueBerry Workbench ready

WilliamFCB commented 3 years ago

guess I need to move to Sourceforge MITK mailing list for feedback thanks

peterneher commented 2 years ago

Hi @WilliamFCB . Sorry for not getting back to you, I was on parental leave until recently. Did you get your answer on the mailing list? If not, I am happy to look into this.

peterneher commented 2 years ago

When looking at your first post, it seems like you did not install MITK Diffusion but the regular MITK Workbench. For dMRI processing, fiber tractography and specifically also for handling .trk tractography files, you need MITK Diffusion.

You will find the download link in the readme of this repository: https://github.com/MIC-DKFZ/MITK-Diffusion#Downloads