On 12/5/2020 2:16 AM, Wei Shao wrote:
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Hello, Freesurfer team
This is Wei Shao, I was trying to convert the freesurfer automatic segmentation of the hippocampus subfield into native space so I can compare it with the manual segmentation.
Here is the command: mri_label2vol --seg lh.hippoAmygLabels-BAYXXXXX-T2.v21.CA.mgz --temp rawavg.mgz --o lh.hippo-BAYXXXXX.mgz --regheader aseg.mgz
1 Could you tell me which files I should use in terms of the temp and regheader flag. Template is fine, but use lh.hippoAmygLabels-BAYXXXXX-T2.v21.CA.mgz for --regheader
2 the manual segmentation based on T2 image, do I need to use the same T2 image as the overlaid image when it comes to Freeview? I think the nu.mgz is T1 image, could you tell me where I can find the T2 image accordingly? I'm not sure what you mean here.
3 do you know any command that can help me to check the information of the .mgz file like the 3dinfo command? Try mri_info
I really appreciate your help, Thanks.
Best, Wei
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