Hi again,

I realized that it may be helpful if I include some images to show what I mean when I say “slightly offset”. In the image attached are 2 T1w images overlayed with the right WM thresholded from the aparc+aseg image. On the left is the native space, and the right is in FS space. You can see a slight shift in the segmentation on the left compared to the native space on the right. (I’m using the thresholded WM from the aparc+aseg because it’s easier to see the offset than with the entire segmentation).

Please let me know if you have any suggestions for how to correct this!

Katie Larson

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Larson, Kathleen E
Sent: Wednesday, April 7, 2021 4:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] aparc+aseg to native space issue

Hi,

I am having an issue converting the aparc+aseg segmentation into the native space. I have tried using both of the following commands:

mri_label2vol --seg aparc+aseg.mgz --temp rawavg.mgz --o aparc+aseg_native.mgz --regheader

mri_vol2vol --mov aparc+aseg.mgz --targ rawavg.mgz --regheader --nearest --o aparc+aseg_native.mgz

In both cases, the output segmentation in native space is slightly offset along the x axis (given x,y,z coordinates). In fact, mri_label2vol is offset in the opposite direction as mri_vol2vol. All outputs have the same origin as the original native space, so I am wondering if it’s a problem with the interpolation. Do you have any advice for how to fix this issue?

Thank you!

Kathleen Larson (she/her)

Medical Image Computing Lab (MedICL)

Biomedical Engineering | Ph.D. Candidate

Vanderbilt University