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neuropoly / template

A framework for creating unbiased MRI templates of the spinal cord
MIT License
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Take into account min and max disc label option from configuration file into code #41

Closed NadiaBlostein closed 11 months ago

NadiaBlostein commented 1 year ago

Context

Currently, it is possible to specify the min/max of labels from the config file, see here:

https://github.com/neuropoly/template/blob/81e9d93763886f0d2e2610e1a0537d427ef2a166/configuration_default.json#L7-L8

What is missing though is: the ability to make use of the information entered in the config file.

Solution

Modify the following files: https://github.com/neuropoly/template/blob/master/preprocess_normalize.py

jcohenadad commented 11 months ago

depends on #60

NadiaBlostein commented 11 months ago

We decided to only include last_disc in configuration.json! And last_disc part depends on issue #60, refer to that to see the fix.

jcohenadad commented 11 months ago

pls open another issue to address the "first_disc" that needs to go in config json at some point

NadiaBlostein commented 11 months ago

Fixed in branch nb/issues_59_and_41, commit cd8b936faa31d5a1bba63b15937e20bc5a87b319