You can get the volume from the aseg.stats file. Unfortunately, we do not 
separate the lesions into left and right. You could do something like
mri_binarize --i aseg.mgz --match 77 --o wmlesions.mgz
mri_volcluster --i wmlesions.mgz --sum lesions.sum.dat --thmin 0.5 --regheader 
This will output a list of lesions clusters in lesions.sum.dat and their 
coordinates. you can see which ones are left and with ones are right.

On 9/3/2019 5:17 PM, Sam W wrote:

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I have run recon-all on T1 scans of patients with WM lesions. I noticed however 
that for some patients the lesion is excluded from aparc.a2009s+aseg.mgz but 
for other patients it is included (and labelled as non-lesion).
Ultimately I'd like to extract a) volume information in WM and b) volume 
information of the WM lesion. I think I can get the the WM volume from the 
wmparc.stats file. For the lesion volume I think I can take the 
WM-hypointensities from the aseg file right? However I noticed that if a lesion 
is on the right hemisphere, the Right-WM-hypointensities shows 0s in all 
columns, which cannot be right.
I have a mask of the lesion (1s where lesion occurs, 0s elsewhere) in 
anatomical space, can I use this mask somehow in FS to inform recon-all where 
the lesion occurs?
Thanks in advance!

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