There is  not an easy way to do this. FS expects an intact whole brain,
and it tries to fit such into every brain, ie, it is trying to force a
whole cerebellum where there is none. What some people do is to fill the
lesion with "reasonable" intensities, eg, from the contralateral side.
Eg, you could left-right reverse the subject:
mri_convert orig.mgz --left-right-reverse-pix orig.lrrev.mgz
mri_coreg --mov orig.lrrev.mgz --targ orig.mgz --reg lrrev.lta
mri_vol2vol --mov orig.lrrev.mgz --targ orig.mgz --reg lrrev.lta --o
orig.lrrev-in-orig.mgz
Then replace the voxels in the lesion in orig.mgz with voxels from
orig.lrrev-in-orig.mgz and re-run
Let me know how it goes

On 9/18/19 6:52 PM, Sam W wrote:
>
>         External Email - Use Caution
>
> 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 <mailto: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:
>>
>>             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
>>
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