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Dear Freesurfers I segmented the given example subject 'bert' by using the command (following the steps https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures) Step-1: recon-all -all -s bert -brainstem-structures Step-2: recon-all -s bert -brainstem-structures Step-3_a: mri_vol2label --c $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.mgz --id 173 --l midbrain_vt.label Step-3_b: mri_vol2label --c $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.FSvoxelSpacemgz --id 173 --l midbrain_vx.label
Now when i view the label file along with the respective segmented volumes, the results i get for both the vertex domain and voxel domain, does not cover the whole midbrain. as shown below.
freeview -l midbrain_vt.label -v $SUBJECTS_DIR/bert/mri/nu.mgz -v $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.mgz:colormap=lut [image: image.png]
freeview -l midbrain_vx.label -v $SUBJECTS_DIR/bert/mri/nu.mgz -v $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.FSvoxelSpace.mgz:colormap=lut [image: image.png]
Question No.1. Please let me know, what is wrong with my steps? Question No.2. Please let me know is it possible to generate label files in voxal space but with better resolution? like vertex space.
Warm Regards,
Safi
