External Email - Use Caution
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:
External Email - Use CautionHello, 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
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/1njESIMg1HmX6gu1X2R1Ge86m18YFogUZa9cR4V22HdolVH...
