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CBICA / CaPTk

Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk
https://www.cbica.upenn.edu/captk
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Core Dump message when using .cwl FeatureExtraction aplication in linux #1408

Closed rafaloz closed 3 years ago

rafaloz commented 3 years ago

Describe the bug Core dump message when using the FeatureExtraction.cwl app in linux Ubuntu 20.04. Also appears when using batch processing. Nonetheless, I can extract the features case by case using the GUI.

To Reproduce Steps to reproduce the behavior:

  1. Install CaPTk
  2. Use FeatureExtraction.cwl

Expected behavior Feature extraction of the case.

Screenshots Screenshot from 2021-04-07 20-05-53

CaPTk Version CaPTk 1.8.1

Desktop (please complete the following information):

AlexanderGetka-cbica commented 3 years ago

Pinging @sarthakpati

sarthakpati commented 3 years ago

Hi @rafaloz,

Thank you for your interest in CaPTk!

Would it be possible to share the parameter file and the mask (not the images) so that we can debug this?

Cheers, Sarthak

rafaloz commented 3 years ago

Sure! The parameter file is the default one with resampling = 1. I attach both, the file and the mask to this message. Files_debugging.tar.gz

sarthakpati commented 3 years ago

Thank you. I will debug and keep you posted.

sarthakpati commented 3 years ago

Hi @rafaloz,

Could you please try with the default parameter file in https://github.com/CBICA/CaPTk/blob/master/src/applications/FeatureExtraction/data/1_params_default.csv?

I believe there are a few values that are needed but are missing. I will put an error check for those, thank you!

rafaloz commented 3 years ago

Tested. Screenshot from 2021-04-08 18-25-45

I didn't checked the part:

Histogram binning type needs to be defined in the parameter file, please see default parameter file for example. Quantization extent needs to be defined in the parameter file, please see default parameter file for example.

since I was using almost the exact parameter file I thought It was not that important

I'll read more carefully next time, thanks for your time sry!

sarthakpati commented 3 years ago

Thank you for making the error checking on our end better! Closing this issue out, please feel free to either re-open this or open a new one if you run into issues. 😄

rafaloz commented 3 years ago

I am having problems using the .cwl still... is there any working parameter file available?

sarthakpati commented 3 years ago

Hi, you can use this: https://github.com/CBICA/CaPTk/blob/master/src/applications/FeatureExtraction/data/1_params_default.csv