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Hello dear all,

I use Freesurfer-Samseg for MS lesion segmentation(cross-sectional).

I use the T1 and Flair for this. (just these are inputs) I registered flair and t1 to DIR for every patient.

(My manual lesion masks are on DIR imaging.) I controlled the registrations

At the beginning i didnt change initial threshold of run_samseg. (default value)

I created a binary lesion mask using different threshold.

threshold 0.1= dice 0,604

threshold 0.05= dice 0.611

threshold 0.001 = dice 0.599

Do you have any recommendations to increase the dice? It seems that with this way It can't go up about 0.6

Best,

Dilek

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