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) http://www.jeiglesias.com

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 [cid:image001.png@01D61E31.A0CE3E30]

freeview -l midbrain_vx.label -v $SUBJECTS_DIR/bert/mri/nu.mgz -v $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.FSvoxelSpace.mgz:colormap=lut [cid:image002.png@01D61E31.A0CE3E30]

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