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 software is that the inputs are in the same space. I mean If you want, you can register inputs even to atlases. That's why I think it doesn't matter to change the reference based on the patient . Since the register mentality is to register to high resolution, I register in different combinations. 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 <dozkan521@gmail.com>, 30 Ağu 2022 Sal, 14:01 tarihinde şunu yazdı:

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. When I try to register my manual mask to new mask created by freesurfer samseg, fsl couldn't recognize the lesions.mgz extension.

Or should I use t1 space for registration? i tried that one. and then, my registration result was really bad.

As a consequence, ho should we deal with mask registration?

Best,
Dilek