@@ -5,8 +5,13 @@ For more information about the QUINT workflow:
https://quint-workflow.readthedocs.io/en/latest/
# Usage
Fill in the test.json with the path to the required input files. e.g. path to reference atlas volume, atlas label file, segmentations (from ilastik), alignment json (from QuickNII or VisuAlign)
Then Run testOOP.py outside of the PyNutil directory to inititate the job.
As input PyNutil requires:
1. An alignment JSON generated with the QuickNII or VisuAlign software
2. A segmented image for each brain section with the feature-of-interests displayed in a unique RGB colour.
To run PyNutil, first fill in a test.json with the paths to the required input files. This includes the reference atlas volume, atlas label file, segmentation directory, and path to the alignment json (from QuickNII or VisuAlign).
Then Run testOOP.py outside of the PyNutil directory (cd ..) to inititate the job.
