brainglobe / brainglobe/brainglobe.github.io

how to edit existing annotations with ITK snap

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Python
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Description

This should take the form of a "How-to" guide in [the diataxis sense](https://diataxis.fr/how-to-guides/).

It should include the required prerequisites:
* ITK snap installed.
* the template that will guide the annotation, as nifti
* the annotations as nifti, in the template space
* an agreed upon, written-down list of regions and their relationship

And the steps will include~
* how to create a new region
* links to some semi-automated segmentation tricks
* how to edit the boundaries of an existing region
* links to some editing tricks
* how to change the colour of an existing region
* how to inspect an annotation
* make sure you look at it from all orthogonal views
* avoid un-annotated pixels inside
* how to save the region-id map

A note that you can also do this with `napari` or other image editing tools if you want, but you will (at least for now) you need to keep track of the region id to region name map yourself in that case.

Contributor guide

Open the contributing guide

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