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hsieh42 / exit_process

Exit process and project boards for tracking issues.
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Run DICOM manipulation in jupyter-notebook with sample data #23

Closed hsieh42 closed 6 years ago

hsieh42 commented 6 years ago

and upload the notebooks.

Sample data: one study from ctDNA and one mammographic study.

hsieh42 commented 6 years ago

See https://github.com/hsieh42/dicom_manipulation/blob/master/anonymization/dicom_manipulation_demo.ipynb

bhaghighi commented 6 years ago

Can we used Jupyter notebook in /cbica/CBIG/comp_space? I am getting this:

HTTP request sent; waiting for response.[I 16:43:05.369 NotebookApp] Accepting one-time-token-authenticated connection from 127.0.0.1 localhost cookie: _xsrf=2|dff4ceff|0cb97770fa0cb8953b0e47b1495b489e|1537994585 Allow? (Y/N/Always/neVer)

bhaghighi commented 6 years ago

All of Script should necessarily be in comp_space of CBIG? For example, do we need to make a folder based on our name if any of us would like to tweak or modify the codes a little bit?
Thanks,

hsieh42 commented 6 years ago

Can we used Jupyter notebook in /cbica/CBIG/comp_space? I am getting this:

HTTP request sent; waiting for response.[I 16:43:05.369 NotebookApp] Accepting one-time-token-authenticated connection from 127.0.0.1 localhost cookie: _xsrf=2|dff4ceff|0cb97770fa0cb8953b0e47b1495b489e|1537994585 Allow? (Y/N/Always/neVer)

Did you try any option? Did it work? jupyter-notebook on the cluster can be sometimes funny. You should report system issue to elog.

hsieh42 commented 6 years ago

All of Script should necessarily be in comp_space of CBIG? For example, do we need to make a folder based on our name if any of us would like to tweak or modify the codes a little bit? Thanks,

@bhaghighi You are welcome to clone a copy of the code in the repo to any location you prefer. Always point the cfg file to the one in /cbica/comp_space/CBIG. If you wish to tweak the code, you can do a pull request.