I’m not sure we have that option in mris_info.
If you do ‘mris_info lh.pial’, it will print vox2ras and vox2ras-tkr. You can
compute tkrRAS to scanner RAS transformation matrix with vox2ras *
inv(vox2ras-tkr).
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of ???
Sent: Wednesday, July 17, 2024 8:18 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] (no subject)
External Email - Use Caution
Thank you very much!
Can the transform matrix be extracted out and imported to the 3d slicer. Thus I
can realize the registration in the slicer
-----原始邮件-----
发件人:"Huang, Yujing" <yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
发送时间:2024-07-15 22:53:40 (星期一)
收件人: "Freesurfer support list"
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
抄送:
主题: Re: [Freesurfer] (no subject)
Freesurfer lh.pial and rh.pial xyz coordinates are reported in tkregister space.
I believe you need to convert tkrRAS to RAS space using vox2ras *
inv(vox2ras-tkr). ‘vox2ras’ and ‘vox2ras-tkr’ matrix are reported in mris_info.
If you are using Freesurfer dev version, these three TAGs (TAG_SURF_DATASPACE,
TAG_SURF_MATRIXDATA, TAG_SURF_TRANSFORMEDSPACE) are available in the surface
files. You can use TAG_SURF_MATRIXDATA to convert [x, y, z] coordinates between
TAG_SURF_DATASPACE and TAG_SURF_TRANSFORMEDSPACE.
Best,
Yujing
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of ???
Sent: Monday, July 15, 2024 5:05 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] (no subject)
External Email - Use Caution
Dear Freesurfer Team
I have extracted the left and right cerebral cortex from the aseg.mgz file
in the 3d slicer.
At the same time, I have loaded the lh.pial and rh.pial in the 3d slicer
the left and right cerebral cortex extracted from the aseg.mgz file was not
in the same position with the lh.pial and rh.pial in the 3d slicer
How should I put them in the same position in the 3d slicer
Thanks
Mengjun
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