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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
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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 CautionDear 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
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Thankyou, Sir. It really helped me a lot.
On Sat, Apr 20, 2019 at 11:46 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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 CautionDear 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
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