What are the voxel sizes in the native space? It may be that if it were shifted one voxel over, it would be shifted too far in the other direction.

On 4/12/2021 10:42 AM, Larson, Kathleen E wrote:

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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

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