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shimming-toolbox / tissue-to-MRproperty

Assign magnetic resonance property values to segmented anatomy
GNU General Public License v3.0
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Remove dependency to SCT #6

Open jcohenadad opened 2 weeks ago

jcohenadad commented 2 weeks ago

Code should not be dependent on SCT. All you should need to run the code is Python and a label file.

https://github.com/shimming-toolbox/segmentation-to-MRproperties-converter/blob/2eef20de25762b53972042b127bdeab32f968b46/interactive.ipynb#L206-L210

sriosq commented 2 weeks ago

Hello, the code is not dependent of SCT. I added that section to explain how one can add labels, and as an example, I used SCT. Perhaps I should re-write the text? Thank you :)

jcohenadad commented 2 weeks ago

In general it is a good idea to avoid 3rd party dependency when creating a tutorial for a software-- eg what if a user only does brain studies, why would you ask them to install SCT?

sriosq commented 2 weeks ago

Okay I see. In my example I used _sctmaths to workaround adding the labels but I see that this could be done in many different ways hence SCT shouldn't be a requirement. Do you recommend taking out the example code and leaving just an explanation on the README file?

jcohenadad commented 2 weeks ago

Do you recommend taking out the example code and leaving just an explanation on the README file?

Yes-- or you could show how to do is with a simple image editor (eg ITKsnap, Slicer)

sriosq commented 1 week ago

I did some changes to the explanation of adding a label here: https://github.com/shimming-toolbox/tissue-to-MRproperty/commit/a4688ef4d139ad6cc58a192cbe3f3608915750e8 I specify that I use SCT only as an example and I elaborate more on whats the strategy to adding the labels and that it can be done with any tool. Looking forward to your opinion on this, thanks again for the feedback! @jcohenadad

sriosq commented 1 week ago

I removed the dependency here https://github.com/shimming-toolbox/tissue-to-MRproperty/commit/10ea7ab61d91d954d45f992e218fedd510c9b291 For label editing and adding I know refer to a "strategies" repo under my profile. Thanks for feedback @jcohenadad