Re: [Freesurfer] samseg ground truth's space

2022-08-30 Thread Dilek Özkan
External Email - Use Caution Even if I register 2d T1 to 3D Flair? (form low res to higher res; such as 2D T1: 1*1*5, 3D Flair: 1*1*1) Douglas N. Greve , 30 Ağu 2022 Sal, 17:30 tarihinde şunu yazdı: > If you resample the t1 to another space, it might get blurrier. > > On

Re: [Freesurfer] samseg ground truth's space

2022-08-30 Thread Douglas N. Greve
If you resample the t1 to another space, it might get blurrier. 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

Re: [Freesurfer] samseg ground truth's space

2022-08-30 Thread Dilek Özkan
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 give two inputs to the software. The rule that applies to every

Re: [Freesurfer] samseg ground truth's space

2022-08-30 Thread Douglas N. Greve
If you want to  use FSL, you will have to convert to nifit, eg, mri_convert file.mgz file.nii.gz On 8/30/2022 7:01 AM, Dilek Özkan wrote: External Email - Use Caution Hello dear all, I want to use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I got the T1 and

[Freesurfer] samseg ground truth's space

2022-08-30 Thread Dilek Özkan
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.