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hsieh42 / exit_process

Exit process and project boards for tracking issues.
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ctDNA workflow and analysis #20

Closed hsieh42 closed 6 years ago

hsieh42 commented 6 years ago
BardiaYou commented 6 years ago

Michael, Could you please add a demo of what you have kindly shown in the meeting, how to get start with converting the process (in the DICOM anonymization)? I already have "dicom_manipulation-master/anonymization", and want to continue using the toolbox. Thank you

hsieh42 commented 6 years ago

A note book is in the repo. Please see

https://github.com/hsieh42/dicom_manipulation/blob/master/anonymization/dicom_manipulation_demo.ipynb
BardiaYou commented 6 years ago

Thanks! Really helpful.

BardiaYou commented 6 years ago

I have a small problem running "run remove_dicom_fields.py -h", "show_dicomdir.py", I am receiving the syntax error. (Put my codes (here) and the files (here) ). Thank you for your help!

hsieh42 commented 6 years ago

when you do run some_code.py you need to make sure that the code is either in the path or that you are in the directory where some_code.py is. To run codes in dicom_manipulation-master/anonymization you need to navigate into that directory. In cell 35, it shows that you are in dicom_manipulation-master therefore you can only run read_dicom_header.py or sortdicom.py but not codes in dicom_manipulation-master/anonymization.

BardiaYou commented 6 years ago

Thanks for the help! I have given the address properly but " cd ".....\Codes\dicom_manipulation-master\anonymization" run remove_dicom_fields.py -h " and again received this message: File "", line 1 cd "......\Codes\dicom_manipulation-master\anonymization" ^ SyntaxError: invalid syntax

hsieh42 commented 6 years ago

Multiple dots in a relative path are invalid. A valid way to go up one level is two dots followed by a slash.

BardiaYou commented 6 years ago

Yes, I did not use it with dots. I used it as mentioned below: cd "C:\Users\YousefiB\Documents\Codes\dicom_manipulation-master\anonymization"

but received an error: File "", line 2 run remove_dicom_fields.py -h ^ SyntaxError: invalid syntax

hsieh42 commented 6 years ago
  • Data collection
  • DICOM sort and conversion to nifti
  • How to read RECIST report from MINT
  • itk-snap segmentation
  • PyRadiomics
  • Analyses using jupyter-notebook
  • Survival analysis

Please find the analyses and slides in https://github.com/hsieh42/ctDNA. Closing the issue as we have discussed the whole project on 9/26/2018. Please create new issue should you encounter any.