Dear FS experts,

I am testing out which threshold works the best for the image. As I tested 0.3 and 0.9, the lesion masks do show the difference but the measurement is the same. Please see below for your information:

Fig 1. Lesion.mgz with a threshold of 0.3 applied to FLAIR image 

Fig 2. Lesions.mgz with a threshold of 0.7 applied to FLAIR image

Do the volume of lesions supposedly different with threshold adjustments? 

The following code is what I used for running samseg:

run_samseg --input $FREESURFER_HOME/${i}.nii $FREESURFER_HOME/${i}_flair_reg.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --threshold 0.7 --output $SUBJECTS_DIR/${i}_samsegOutput_thold0.7/ --save-posteriors --threads 8

Thank you for your attention.