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 subject 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: External Email - Use Caution 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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