Thanks Doug. The problem is that for some patients the lesion affects the segmentation dramatically. For example I have one patient with a large lesion in the right cerebellum which is partly in GM and partly in WM. If I load the aseg file I see that a portion of the right cerebellar hemisphere is assigned to the left cerebellar hemisphere (the right white matter is also being assigned to the left hemisphere) and the whole cerebellum looks distorted. I suppose there is no way to inform freesurfer about the lesion during recon-all?

I followed the steps in the FsTutorials for the cerebral cortex, but how can I do the same for the cerebellum patient? What is the recommended way to fix a bad segmentation due to cerebellum lesions? Control points, white matter edits, or something else?

Sam

On Fri, Sep 6, 2019 at 4:28 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

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:
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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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