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. 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
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 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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
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 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dgreve@mgh.harvard.edu, 30 Ağu 2022 Sal, 17:30 tarihinde şunu yazdı:
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 CautionI 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
Freesurfer mailing listFreesurfer@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/13WempIGiCj_JHbjJcI9KGCY7Eb1-nbdj5FSaLHyOd-PNR3... 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/1fxSl-e5OVCBum-OUcvZhRU2RfU7purJZPrl_tqP7kSUTZa... < https://secure-web.cisco.com/1fxSl-e5OVCBum-OUcvZhRU2RfU7purJZPrl_tqP7kSUTZa... .
freesurfer@nmr.mgh.harvard.edu
-
Dilek Özkan -
Douglas N. Greve