Hello again,

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, thea are true.

I created a binary lesion mask using different threshold. (mri_binarize --i /data/projects/MS_MRI/posteriors/Lesions.mgz --o /data/projects/MS_MR/binarize/lesion_binary.mgz --min 0.01)

I checked the dice score with ground truth values with python.

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?

# cvs_version 7.2.0

# sysname Linux

# machine x86_64

Douglas N. Greve <dgreve@mgh.harvard.edu>, 31 Ağu 2022 Çar, 00:12 tarihinde şunu yazdı:

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On 8/30/2022 12:51 PM, Dilek Özkan wrote:
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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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