I'm not sure I understand what your goal is. Are you just trying to visualize specific brain structures over your input image? Are you interested in segmentation maps or binary segmentations?

If you want to visualize segmentation maps, you can just use Freeview and load the specific structure file(s). Note that these segmentation maps are 1) not binary, i.e., they have values *between* 0 and 1, and 2) they are in the same space as your input image.

If you want to visualize binary segmentation for specific structures you can do this in Freeview. You load your segmentation (seg.mgz) as a lookup table and select only the label values that you're interested in.

Da: Giulio Siracusano <giuliosiracusano@gmail.com>
Inviato: domenica 27 novembre 2022 04:01
A: Cerri, Stefano <SCERRI@mgh.harvard.edu>; freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Oggetto: Re: [Freesurfer] SAMSEG Lesion images not written

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Hi Stefano,

I'd like to ask you a question wrt SAMSEG.

I'd like to extract segmentation maps using SAMSEG, and I know already that we have to use '--save-posteriors' option when running the command.

They will be saved in the samseg output directory under the "posteriors" folder.

How is it possible, starting from these binary segmentation maps, creating multiple images of the brain where a given (segmentated) region is highlighed?

In order to do that, you have to multiply a given reference brain images -over- each segmentation map (which is a binary matrix with 0's and 1's).

What is the reference brain image all these segmentation maps are related to?

I hope to be clear enough

Best regards

Giulio Siracusano