[Freesurfer] Samseg dice is low

External Email - Use Caution 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

Re: [Freesurfer] samseg dice score is low

CHrt3Y-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 dea

[Freesurfer] samseg dice score is low

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

Re: [Freesurfer] samseg ground truth's space

; On 8/30/2022 9:46 AM, Dilek Özkan wrote: > > External Email - Use Caution > I decided to register T1 and Flair to DIR at the beginning. with this way, > I will get the new mask in already DIR's space which means manually > segmented masks' space. > > In my case, I will g

Re: [Freesurfer] samseg ground truth's space

. My ınputs will not change. t1 and flair. But, If I have a 3d Flair, I register t1 to flair. If I have a 3d t1,then I register flair to t1. Is there something wrong here? Best, Dilek Dilek Özkan , 30 Ağu 2022 Sal, 14:01 tarihinde şunu yazdı: > Hello dear all, > > I want to use Freesurf

[Freesurfer] samseg ground truth's space

External Email - Use Caution Hello dear all, I want to use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I got the T1 and Flair for this. I registered *flair to t1 *for every patient. My manual lesion masks are on DIR imaging. I am using FSL for registration.

[Freesurfer] samseg inputs

External Email - Use Caution Hello dear all, I want to use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I have read the paper, accordingly I want to try the t1-flair combination in terms of the accuracy. Do you have any experience with T1 images with contrast

[Freesurfer] lesions number and lesion volume of MS with samseg

External Email - Use Caution Hello dear all, I want to use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I have ground truth values(binary mask), lesions number and lesion volume. I will compare these with the output of freesurfer-samseg. I am confused about

[Freesurfer] samseg lesions labels and values

External Email - Use Caution Hello dear all, I want to use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I have read that I need to add "--save-posteriors Lesions" to run_samseg to obtain lesion probabilities. 1)In the stats file I can see the value of "Lesions"