How to generate Label files for Atlas Segmentation?

I am trying to generate labels for different regions to do label Registration 3 D in Atlas tool kit. I could get output for first label only but not able to generate the combined output with all regions. Please advice me how to generate different label.tiff files for atlas 3D label registration.

You can use the Segmentation Editor plugin.

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I am using segmentation editor for generating the labels. I could generate all labels for various regions but when I do 3D label registration it can do processing on first region only. It won’t show all the regions in segmented output.

Have you tried contacting the authors of the Atlas toolkit?

Hi Sonali,

I touched on this in my reply to your earlier question:

The Label Registration 3D tool currently allows you to select only one region for registration. You can see in the screen cast that the ‘Select Channel (0-255)’ parameter is set to one (meaning the first labelled region).

In theory, you could apply the resulting transformation (".ots" file) to the original label (".label" file) using the tool Apply Label Registration. However, you should bear the following in mind:

  • The LUT data will be stripped from the label file during the transformation (should be able to fix that in a future update), so the different regions (red, green, blue etc.), which each have a different pixel value (1, 2, 3 etc.) will be shown as very dark grey. You can correct the colours of the labels using the LUT editor (Image>Color>Edit LUT).

  • The underlying bUnwarpJ plugin interpolates pixel values during the transformation, so pixels at the edge of label two (pixel value = 2) will be re-assigned to label one (pixel value = 1), etc.

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