External Email - Use Caution 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 <dgr...@mgh.harvard.edu>, 31 Ağu 2022 Çar, 00:12 tarihinde şunu yazdı: > Hi Dilek, your bug report is incomplete. Please see > https://secure-web.cisco.com/1RnsI-tf_KXbBLM99OHi9vq19avjAsCHrt3Y-Vc96p1_VmCoC9eioH_VbD57wn2rDDSEgXjKDACMfDuZmmHjAEJxeOvKdAufIk1i5bI7uo7LQCeN7gcTdWN5Qgwgb3VfBe5NxPxmbNpisuiBfrRdwhTOElk0u6PfrN67B4ClcL0Nfc3lCQfiwnBKlENUpfXTfiFtl3sJwobngzeaduTd5bc7FXECIeZjYRKuok8IJ052pqSATiOrchNlrKmcJ0dDeQeIP77SH61FGi8cdapM14PqqlIp3-98d1QVoylKc1tRCecBmzdB5lmzwqGmma7R4/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting > for how to file an > informative bug report. > > On 8/30/2022 12:51 PM, Dilek Özkan wrote: > > External Email - Use Caution > 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 > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1dSWiJHKqOhrJfz5sKbVln8b3KW6dGwCZyQq8DhuebSXUBb26sfRPFDU5IwDGDZrMXPO6ie6omKVDx5EALqtaabU9pT17yNrXgEe1K0Rmd9_jUSche6zd2PFZSiSxmnJMZdfoiluMuqyVgm0DDUpnSzw546Pma6RKkImZQ6-i9rqcdx6PP8jbaig3-liIUkhfMtOo522iei0kJuOECv8W7SjnLc6ImvD1pRlJ6OWVxBEPoFkUaBByxxig69BDf9YqEyE15-UkTkKs3ioC41r2J1LEq9ANICQHOb4uUshXgLG4_pJ-hYAs54aDDf3kDQcQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/1OfvRD_0W4TURHltDGjSi5_vIXm45BvIbmcwZsafnaNyejOfUojiWy8SdIiRPyK0unxNETwAwHEW-Xjysq2zZEHSVAyeptow7ZklPJHvCCFegGpBV4-Wonc5UlsjoXsriIGlQjzp9x1h9jjsLHiV5zKCh3IKf7NGkI7E86MEOY925C7qDM-CiZXWpSex_W_B2PJLq37W1lrQjh6gMbqX4T0aOfefiRSrlRSs6D-C5BFqdhswBwSDAjKHHMGVY4Vq2HYQjPEk4mZsMWBHbn1sJmr5bw55CldqjfmeKN3E_A0QFxxOoGkSLQDQT6GTwsvKl/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1OfvRD_0W4TURHltDGjSi5_vIXm45BvIbmcwZsafnaNyejOfUojiWy8SdIiRPyK0unxNETwAwHEW-Xjysq2zZEHSVAyeptow7ZklPJHvCCFegGpBV4-Wonc5UlsjoXsriIGlQjzp9x1h9jjsLHiV5zKCh3IKf7NGkI7E86MEOY925C7qDM-CiZXWpSex_W_B2PJLq37W1lrQjh6gMbqX4T0aOfefiRSrlRSs6D-C5BFqdhswBwSDAjKHHMGVY4Vq2HYQjPEk4mZsMWBHbn1sJmr5bw55CldqjfmeKN3E_A0QFxxOoGkSLQDQT6GTwsvKl/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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