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
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