Hello, I try to segment femoral cartilage. To do so, firstly I crop volume containing the area and then try to segment the cartilage using “Draw”. The problem is that I’m unable to do it - it disappears. A painting option works - it marks the area. Could you help me?

This could happen when the slice view is positioned right at the boundary between two slices. This is not likely to happen if you use latest Slicer Preview Release. If you the issue is not resolved then let us know and we can give further advice.

Hello, As a follow up is it possible to save the 2D annotations into a .json file? I wish to use the annotations to train a model. Thanks as always :slight_smile:

You can get voxels of a segment as a numpy array by calling slicer.util.arrayFromSegment (see an example here ) and save it in any file format you like.

I’ve looked over the code but can’t quite understand. I used the segmentation editor tool to draw annotations free handedly, and it seems like 3d slicer saves them in .nrrd by default. Does the call also work for shapes that are not a fixed polygon?

Also quite relatively new to programming in Python, I would appreciate it if you could guide me through how to save the freehand annotations (2D) into a json file format. I appreciate your time sir.

For clarity, I wish to obtain the coordinates of the annotated region that I drew free-hand. Would such a thing be possible?

[image] caesarsalad: Also quite relatively new to programming in Python, I would appreciate it if you could guide me through how to save the freehand annotations (2D) into a json file format. JSON just specifies low-level syntax for data storage but it does not tell what you store and exactly…

A drawing disappears after Cropping Volume

Support

Topic		Replies	Views
Query on exporting annotation Support	6	456	February 20, 2021
How to annotate X-Ray or CT images and exporting with that/these annotation information(s) ? Support segmentation	4	916	August 11, 2021
Save segmentation output as xml file or binary mask Support	4	2431	February 6, 2019
Export ROI box to json file Support	3	1201	December 31, 2018
Free hand drawing is not working effectively in slicer Support	4	1269	January 13, 2019

A drawing disappears after Cropping Volume

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