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Hello. I am running run_samseg_long on Freesurfer 8.1.0 with longitudinal
MS T1W data and I am trying to resolve lesion undersegmentation. Whenever I
lower --threshold manually (e.g., --threshold 0.2), it seems to ignore it,
outputting "thresholding posterior of Lesions with threshold: 0.3". To try
thresholding manually, I added to the command --save-posteriors and
--save-probabilities, but I'm not exactly sure what the outputted
"Lesions.mgz" files in the posteriors and probabilities folders represent
(and why the "Lesions.mgz" file in the probabilities folder has three
frames). Can I please get advice on how to compute lesion volumes and masks
at a threshold that is lower than 0.3? Thank you!
