How to use the code under python/deepsulci？

[lzhzju]

Thank you for your amazing work. I would like to know how to use the code under python/deepsulci to perform sulci recognition on my own brain data?

[denisri]

Hi,
You normally don't use deepsulci alone, because it's used as a step in the long Morphologist processing pipeline. Deepsulci performs sulci identification, but takes as input the preprocessed data which result from the full segmentation pipeline, so you can't run it on raw images.
If you are interested in how this step works, there is a bit of doc here:
https://brainvisa.info/morpho-deepsulci/dev_doc/
and the easiest starting point is the _run_process() method of the sulci labeling process here:
https://github.com/brainvisa/morpho-deepsulci/blob/master/python/deepsulci/sulci_labeling/capsul/labeling.py

Now if what you want is to run the full Morphologist pipeline from a script/program, the easiest way is to call the command axon-runprocess with appropriate parameters, but it is also possible to call the python API. See:
https://brainvisa.info/axon/dev_doc/

Denis