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Hello, 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! Sam
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