Hi Eugenio,

Yes please give me some advice on the matlab commands for this since I am not very familiar with matlab...

Cheers,

Jacky

Hi Jacky, 
this is a good question, and unfortunately there isn't a great answer to it. 
The volume is computed upong a probabilitic segmentation of the voxels that is 
not written to disk (this is very similar to what happens with aseg.mgz and 
aseg.stats). In order to properly update the volume estimates, you would have 
to know the probability that the inpainted voxels belong to the brainstem as 
estimated by the algorithm, which we don't currently write to disk. 
Another option would be to toss the volumes given by the algorithm, and compute 
new volumes for all cases and brainstem structures using the hard 
segmentations. You would simply have to count the number of voxels labeled as 
midbrain, pons, SCP and medulla for each subject. You can easily do this e.g. 
with Matlab (let me know if you need help with this). 
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: "Jacky Lee" <cyle...@gmail.com> 
To: "Freesurfer support list" <Freesurfer@nmr.mgh.harvard.edu> 
Sent: Monday, May 9, 2016 2:01:53 AM 
Subject: [Freesurfer] Manual correction for brainstem module 

Hi freesurfer experts, 

I have successfully run the brainstem module for some subjects. On visual 
checking, I can see there are voxels with T1 hypointense lesions mislabelled as 
non-brainstem tissue. I manually corrected them on the 
brainstemSsLabels.v10.mgz on Freeview. Then how do I obtain this new corrected 
volume of the brainstem substructures? 

Thanks. 

Regards, 

Jacky