What command did you use to apply the transform? If mri_convert add -rt nearest to your command line.

The issue is that you are using trilinear interpolation our a label map instead of nearest neighbor

On Apr 20, 2019, at 5:22 AM, Sadia Sheikh <sheikh.sadia14@gmail.com> wrote:

        External Email - Use Caution        

Dear FreeSurfer experts

I did brainstem segmentation using BrainstemSubstructure method. Then after segmentation, I aligned all my segmented brainstem to Talairach coordinates using transform=$SUBJECTS_DIR/$s/mri/transforms/talairach.xfm.

Alignment seems to be fine. But the boundary of the aligned brainstem looks distorted with different other colors. Why does the boundary look like this? and how can I improve this?

I have attached the image of brainstem after alignment.

Thanks in advance.

Regards 

Sadia

Research Student

I’m protected online with Avast Free Antivirus. Get it here — it’s free forever.

<Capture.JPG>

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer