Dear Safi,
The transition between the midbrain and the ventralDC is somewhat geometric and arbitrary; you can look at the details in the paper. Other than that, I don’t think there’s anything wrong!
If you want a surface mesh, you can extract it from the segmentations (eg with mri_mc)
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Safi Ullah ." <safi.ullah@uog.edu.pk>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, April 29, 2020 at 01:20
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] midbrain segmentation does not cover the whole area
External Email - Use Caution
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
freeview -l midbrain_vx.label -v $SUBJECTS_DIR/bert/mri/nu.mgz -v $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.FSvoxelSpace.mgz:colormap=lut
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