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Hello,
Inferior portion of cerebellum are not segmented well. It is included in skullstrip and I tried adding control points in cerebellar WM but this did not help. I am not interested in cerebellum but I do need eTIV. Will this poor cerebellar segmentation affect eTIV calculation?
Thank you,
Carlos
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在 2024-01-06 04:11:28，"Carlos Alcocer" cda33@cornell.edu 写道：
External Email - Use Caution
Hello,
Inferior portion of cerebellum are not segmented well. It is included in skullstrip and I tried adding control points in cerebellar WM but this did not help. I am not interested in cerebellum but I do need eTIV. Will this poor cerebellar segmentation affect eTIV calculation?
Thank you,
Carlos
Here is an explanation of etiv calculation in Freesurfer - https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
etiv is not obtained via direct segmentation of all structures within the skull boundaries. Rather, its estimation depends on the linear transform between the T1 image and a T1w atlas.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Carlos Alcocer Sent: Friday, January 5, 2024 4:11 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] poor inferior cerebellum segmentation
External Email - Use Caution Hello,
Inferior portion of cerebellum are not segmented well. It is included in skullstrip and I tried adding control points in cerebellar WM but this did not help. I am not interested in cerebellum but I do need eTIV. Will this poor cerebellar segmentation affect eTIV calculation?
Thank you,
Carlos
You can try using mri_synthseg --i orig.mgz --o synthseg.mgz it generally does a better job on cerebellum than the native FS command
On 1/5/2024 4:11 PM, Carlos Alcocer wrote:
External Email - Use Caution
Hello,
Inferior portion of cerebellum are not segmented well. It is included in skullstrip and I tried adding control points in cerebellar WM but this did not help. I am not interested in cerebellum but I do need eTIV. Will this poor cerebellar segmentation affect eTIV calculation?
Thank you,
Carlos
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Carlos Alcocer -
Douglas N. Greve -
Huang, Yujing -
李锦光