Here it is (open access)
http://www.sciencedirect.com/science/article/pii/S1053811915001895
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Mohamad J. Alshikho" <malshi...@mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Tuesday, January 26, 2016 4:25:35 PM
Subject: Re: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}
Bruce and Juan,
Thanks a lot for your quick answer. I have one more question please:
What are the anatomical definitions that the brain stem module uses in order to
segment the brain stem. If you can point me to a reference that can help me to
understand this point this will be great!!
Thanks again
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
[e.igles...@bcbl.eu]
Sent: Tuesday, January 26, 2016 10:16 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}
Dear Mohamad,
The brainstem module uses different anatomical definitions than aseg/wmparc,
and yes, the largest discrepancy is in the midbrain.
For the midbrain, I like the segmentation from the brainstem module better,
since it is based on manual annotations made by UCSF collaborators working
explicitly on the brainstem regions. But Bruce's opinion might be different?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Mohamad J. Alshikho" <malshi...@mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Tuesday, January 26, 2016 4:05:24 PM
Subject: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}
Dear Freesurfers,
After segmenting the brain stem using FS6 tools. I used Free view to visualize
the final images. In Free view I opened "orig.mgz", "wmparc.mgz" and
"brainstemSsLabels.v10.mgz" Then I tried to check the segmented structures by
flipping the images.
I noticed an overlap between Ventral DC ( left and right) and mid brain ( as an
output of brain stem segmentation).
I "wmparc.mgz" atlas: Ventral DC and brain stem are totally different segments.
Now After segmenting the brain stem. I see that the Ventral DC belongs to the
mid brain.
Is this natural?
Thanks in advance for any suggestion!
Mohamad
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