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OpenHeartDevelopers / CemrgApp

An Interactive Medical Imaging Platform with Image Processing and Computer Vision Toolkits for Cardiovascular Research.
http://www.cemrgapp.com
BSD 3-Clause "New" or "Revised" License
18 stars 8 forks source link

Interpolation #66

Open nbodagh opened 2 years ago

nbodagh commented 2 years ago

I'm having an issue CEMRG. When I try to segment and change the interpolation to 3D the program crashes

Have you ever had anyone have this before?

Wed Jul 6 14:47:19 2022 Debug: org.commontk.eventadmin.LogLevel=2 in ctkEAConfiguration::startOrUpdate, C:\dev\build\CEMRGapp\ep\src\CTK\Plugins\org.commontk.eventadmin\ctkEAConfiguration.cpp:215 Wed Jul 6 14:47:19 2022 Debug: org.commontk.eventadmin.CacheSize=30 in ctkEAConfiguration::startOrUpdate, C:\dev\build\CEMRGapp\ep\src\CTK\Plugins\org.commontk.eventadmin\ctkEAConfiguration.cpp:217 Wed Jul 6 14:47:19 2022 Debug: org.commontk.eventadmin.ThreadPoolSize=20 in ctkEAConfiguration::startOrUpdate, C:\dev\build\CEMRGapp\ep\src\CTK\Plugins\org.commontk.eventadmin\ctkEAConfiguration.cpp:219 Wed Jul 6 14:47:19 2022 Debug: org.commontk.eventadmin.Timeout=5000 in ctkEAConfiguration::startOrUpdate, C:\dev\build\CEMRGapp\ep\src\CTK\Plugins\org.commontk.eventadmin\ctkEAConfiguration.cpp:221 Wed Jul 6 14:47:19 2022 Debug: org.commontk.eventadmin.RequireTopic=true in ctkEAConfiguration::startOrUpdate, C:\dev\build\CEMRGapp\ep\src\CTK\Plugins\org.commontk.eventadmin\ctkEAConfiguration.cpp:223 Wed Jul 6 14:47:19 2022 Debug: org.commontk.eventadmin.LogLevel=2 in ctkEAConfiguration::startOrUpdate, C:\dev\build\CEMRGapp\ep\src\CTK\Plugins\org.commontk.eventadmin\ctkEAConfiguration.cpp:215 Wed Jul 6 14:47:19 2022 Debug: org.commontk.eventadmin.CacheSize=30 in ctkEAConfiguration::startOrUpdate, C:\dev\build\CEMRGapp\ep\src\CTK\Plugins\org.commontk.eventadmin\ctkEAConfiguration.cpp:217 Wed Jul 6 14:47:19 2022 Debug: org.commontk.eventadmin.ThreadPoolSize=20 in ctkEAConfiguration::startOrUpdate, C:\dev\build\CEMRGapp\ep\src\CTK\Plugins\org.commontk.eventadmin\ctkEAConfiguration.cpp:219 Wed Jul 6 14:47:19 2022 Debug: org.commontk.eventadmin.Timeout=5000 in ctkEAConfiguration::startOrUpdate, C:\dev\build\CEMRGapp\ep\src\CTK\Plugins\org.commontk.eventadmin\ctkEAConfiguration.cpp:221 Wed Jul 6 14:47:19 2022 Debug: org.commontk.eventadmin.RequireTopic=true in ctkEAConfiguration::startOrUpdate, C:\dev\build\CEMRGapp\ep\src\CTK\Plugins\org.commontk.eventadmin\ctkEAConfiguration.cpp:223 Wed Jul 6 14:47:19 2022 3.14 core.mod.core.log: Logfile: C:/Users/nboda/AppData/Local/KCL/CemrgApp v2.1_1584152459/data/11/mitk-0.log 3.38 ERROR: BlueBerry Workbench not running! 3.85 BlueBerry WARNING: Could not get plug-in resource: CemrgAppQtHelpCollection.qhc

OrodRazeghi commented 2 years ago

@nbodagh just to find the root cause, were you actively segmenting the image, when the 3D interpolation was on? or the crash happened after you were done with the segmentation and just wanted to see the final result?

nbodagh commented 2 years ago

I had finished the segmentation and wanted to see the final result

nbodagh commented 2 years ago

Now whenever I try to change it to 3D before I start segmenting, the programme crashes

nbodagh commented 2 years ago

Hi, just writing to ask - do you have any idea about what could be causing this?

OrodRazeghi commented 2 years ago

What is the file format for the image you are trying to segment? nifti? What is the resolution of your image? Is it a really high-res image?

nbodagh commented 2 years ago

Yes, it was nifti and they were high res images. Its strange because it was letting me do it before

OrodRazeghi commented 2 years ago

try downsampling the image to a lower res, and see if it resolves the issue. If you can, please also try segmenting directly on the MITK workbench, and let us know if you face a similar crash.

nbodagh commented 2 years ago

Hi, sorry I'm fairly new to CEMRG. How do I do both of those?

OrodRazeghi commented 2 years ago

You don't have to use CemrgApp to do the resampling, you can use ITKSnap or any similar image processing software that you are familiar with, if you want to use CemrgApp, there is a basic image processing plugin, which you can use for resampling images. One important detail is that the image you are segmenting should be a nifti with the .nii extension. Some docs and tutorials on using the segmentation tools in the scar plugin: sop, video.