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.sadi...@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
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