Hi Dilek,
0.2 Dice seems extremely low. Also, in my experience, a threshold of 0.05 on T1w-FLAIR scans will show up many FP lesions.
We usually reported a Dice in the range of 0.50-0.65 on various datasets (MS and WMH, default threshold, T1w-FLAIR), so I'm surprised by a such low value.
Can you share with us your run_samseg command?
Stefano
Date: Sun, 4 Sep 2022 15:53:17 +0300 From: Dilek ?zkan dozkan521@gmail.com Subject: To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: CAPQSyvLqkvjk7JFxFoAG8RcX7ff40TS70vzvF6uWWHwC6CgqEg@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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Hello 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, these are true.
I created a binary lesion mask using *threshold 0.05. *(mri_binarize --i /data/projects/MS_MRI/posteriors/Lesions.mgz --o /data/projects/MS_MR/binarize/lesion_binary.mgz --min 0.05) I checked the dice score with ground truth values with python.
*threshold *0.05= *dice* 0,2 of the dataset
Do you have any recommendations to increase the dice?
# cvs_version 7.2.0 # sysname Linux # machine x86_64
Best regards