Hello dear all,

I want to use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I have read that I need to add "--save-posteriors Lesions" to run_samseg to obtain lesion probabilities.

1)In the stats file I can see the value of "Lesions" (0.04) But when I try to see on freeview, it says label=99 (lesion label) has no value. So, I can't see the lesions.

2)There are a few labels related to lesions. For example wm lesions;

(498: wmsa, 499: other_wmsa) I have no volume related to these labels neither in my stats file nor on freeview. Should I get only the "Lesions label" for the MS lesion mask?

3)As input, I am using only DIR ımages. I wıill try different thresholds. I have read that by playing mri_binarize and mri_segstats, we can try different thresholds without re-running anything. So, the threshold value required for mri_binarize command refers to the same threshold input in the initial the command of run_samseg?

Best,

Wish