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MedicalImageAnalysisTutorials / SlicerCochlea

Multi-modal cochlea Images registration, segmentation and analysis
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No result with MacOS and missing sample dataset. #38

Closed young-oct closed 1 year ago

young-oct commented 1 year ago

@idhamari I was excited when I found out about this module, and thank you for all your work. I tried to run this module but somehow it's not working. OS: MacOS 13.0.1 (22A400) Slicer Version: 5.2.1

I followed your youtube tutorial here and I want to mention that the datastore module was also deprecated. I wonder if you can include the dataset in github.

Error message from the python interpreter. Defaults paths: VisSimTools folder: /Users/youngwang/VisSimTools Output folder : /Users/youngwang/VisSimTools/outputs elastix binaries are found in /Applications/Slicer.app/Contents/Extensions-31317/SlicerElastix/lib/Slicer-5.2/elastix Cochlea Extension is selected sha256computedCheckSum: 5a1ec154dbf24404ff7357066b8158642fcbd6f159881e7318e9a11975884824 Models or contents are wrong, trying to download ... Downloading VisSim Tools ... Downloading VisSimTools others ... Extracting to user home Error: can not download and extract VisSimTools ... [Errno 2] No such file or directory: '/Users/youngwang/VisSimToolsCochlea'

Screenshot 2022-11-30 at 16 25 40

[Errno 2] No such file or directory: '/Users/youngwang/VisSimToolsCochlea' [VTK] RemoveItem: Failed to find subject hierarchy item by ID 13 [VTK] GetItemName: Failed to find subject hierarchy item by ID 13 [Qt] void qMRMLSubjectHierarchyTreeView::deleteSelectedItems() : Failed to remove subject hierarchy item (ID: 13 , name: ) [FD] 2022-11-30 16:15:06.177 Slicer[746:7532] IMKClient Stall detected, please Report your user scenario attaching a spindump (or sysdiagnose) that captures the problem - (imkxpc_markedRangeValueWithReply:) block performed very slowly (1.70 secs). ..... getting Cochlea location in the input image Fiducial adding event! 0

idhamari commented 1 year ago

Thanks for your interest in our tool. One thing you can try:

move the folder /Users/youngwang/VisSimToolsCochlea/VisSimTools to /Users/youngwang/VisSimTools

If this does not work, please notice that Mac is not supported so it is better to use it on Windows or Linux.

young-oct commented 1 year ago

@idhamari thank you for the wicked quick reply! The tool your group developed is truly awesome. I think the error comes from my dataset(microCT). I got something very nice with the sample dataset I found here. If I could make a suggestion, please update the readme here. Coclea

I also validated this with the zeta dataset provided by https://zenodo.org/record/1473724#.Y4fLxezML0o Once again, great work!

idhamari commented 1 year ago

Thanks, I will close this issue.