External Email - Use Caution
Hi FreeSurfer Developers,
I’m conducting manual ROI labelling on each participant’s inflated surface (after going through the ‘recon-all’ command), but I wasn’t very sure if the coordinates in the corresponding .label files are in MNI 305 space. At the top of the plain text files it’s showing ‘vox2ras=TkReg’.
If they are not in MNI 305, could you please explain a bit about what coordinate system is used here and how I could convert that into MNI 305?
Thank you very much!
Best wishes, Vivian
The coordinates reported in .label are in Freesurfer tkregister RAS space. You can use mri_label2label to map them to MNI 305 space https://surfer.nmr.mgh.harvard.edu/fswiki/mri_label2label
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Yang Yifan Sent: Wednesday, February 5, 2025 8:03 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] FreeSurfer coordinates
External Email - Use Caution Hi FreeSurfer Developers,
I'm conducting manual ROI labelling on each participant's inflated surface (after going through the 'recon-all' command), but I wasn't very sure if the coordinates in the corresponding .label files are in MNI 305 space. At the top of the plain text files it's showing 'vox2ras=TkReg'.
If they are not in MNI 305, could you please explain a bit about what coordinate system is used here and how I could convert that into MNI 305?
Thank you very much!
Best wishes, Vivian
External Email - Use Caution
Hi Yujing,
Many thanks for your reply! The email didn’t come through to my inbox and I just found it in the online archive.
Regarding the coordinate conversion, I had a look at the link but didn’t find MNI 305 related information. It would be very helpful if you could be more specific about the command to run. Thanks!
Best wishes, Vivian
From: Yang Yifan vivian_yyf@outlook.com Date: Wednesday, 5 February 2025 at 13:03 To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: FreeSurfer coordinates Hi FreeSurfer Developers,
I’m conducting manual ROI labelling on each participant’s inflated surface (after going through the ‘recon-all’ command), but I wasn’t very sure if the coordinates in the corresponding .label files are in MNI 305 space. At the top of the plain text files it’s showing ‘vox2ras=TkReg’.
If they are not in MNI 305, could you please explain a bit about what coordinate system is used here and how I could convert that into MNI 305?
Thank you very much!
Best wishes, Vivian
Freesurfer fsaverge is in MNI305 space. Try mri_label2label --srcsubject <> --srclabel <.label> --trgsubject fsaverage --trglabel <fsaverage.label> --hemi rh --regmethod surface
These are some helpful links https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems https://surfer.nmr.mgh.harvard.edu/fswiki/mri_label2label
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Yang Yifan Sent: Friday, February 14, 2025 5:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer coordinates
External Email - Use Caution Hi Yujing,
Many thanks for your reply! The email didn't come through to my inbox and I just found it in the online archive.
Regarding the coordinate conversion, I had a look at the link but didn't find MNI 305 related information. It would be very helpful if you could be more specific about the command to run. Thanks!
Best wishes, Vivian
From: Yang Yifan <vivian_yyf@outlook.commailto:vivian_yyf@outlook.com> Date: Wednesday, 5 February 2025 at 13:03 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: FreeSurfer coordinates Hi FreeSurfer Developers,
I'm conducting manual ROI labelling on each participant's inflated surface (after going through the 'recon-all' command), but I wasn't very sure if the coordinates in the corresponding .label files are in MNI 305 space. At the top of the plain text files it's showing 'vox2ras=TkReg'.
If they are not in MNI 305, could you please explain a bit about what coordinate system is used here and how I could convert that into MNI 305?
Thank you very much!
Best wishes, Vivian
freesurfer@nmr.mgh.harvard.edu
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Huang, Yujing -
Yang Yifan -
Yang Yifan