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Hi, freesurfer team

Thanks for your kind reply!

What I mean in Question 2 is that the manual segmentation is drawing the voxel from T2 images like sub-BAY12044_ses-01_cor_T2w.nii.gz. However, when I convert the freesurfer automatic segmentation(T1 and T2 ) into the native space.

mri_label2vol --seg lh.hippoAmygLabels-BAY12044-T1.v21.CA.mgz --temp rawavg.mgz --o lh.hippoAmy_T1_transfer.mgz --regheader lh.hippoAmygLabels-BAY12044-T1.v21.CA.mgz

mri_label2vol --seg lh.hippoAmygLabels-BAY12044-T2.v21.CA.mgz --temp rawavg.mgz --o lh.hippoAmy_T2_transfer.mgz --regheader lh.hippoAmygLabels-BAY12044-T2.v21.CA.mgz

then, freeview the manual segmentation (20180822_BAY12044_Segmented.nii.gz) and freesurfer automatic segmentation together with or without the colormap, It looks like this

freeview -v nu.mgz -v 20180822_BAY12044_Segmented.nii.gz -v lh.hippoAmy_T1_transfer.mgz

[image: con_5.PNG] freeview -v nu.mgz -v 20180822_BAY12044_Segmented.nii.gz:colormap=lut -v lh.hippoAmy_T1_transfer.mgz:colormap=lut

[image: con_6.PNG]

freeview -v nu.mgz -v 20180822_BAY12044_Segmented.nii.gz -v lh.hippoAmy_T2_transfer.mgz

[image: Com_1.PNG]

freeview -v nu.mgz -v 20180822_BAY12044_Segmented.nii.gz:colormap=lut -v lh.hippoAmy_T2_transfer.mgz:colormap=lut

[image: con_3.PNG]

For some reason, I can't freeview the manual segmentation_T2 images and freesurfer automatic segmentation (T1 and T2 both ) at the same space. Could you help me with that? Thanks!

Best, Wei

On Mon, Dec 7, 2020 at 10:29 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:

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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