If they are aligned in tkregisterfv, then you can use use --regheader
instead of --reg something.lta
On 9/24/19 7:10 PM, Sam W wrote:
>
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>
> Hi Doug,
> anat is a T1w image and is well aligned with orig when I run the
> tkregisterfv command.
> But I suspect
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Hi Doug,
anat is a T1w image and is well aligned with orig when I run the
tkregisterfv command.
But I suspect I know what the problem might be. When I run
mri_vol2vol --mov /data/sub01/anat.nii --fstarg --reg /data/sub01/reg.lta
--o anat-in-fs.mgz --s
mri_coreg should have printed out tkregisterfv command. Try running that to see
if the registration is accurate. What is the nature of anat.nii?
On 9/20/2019 4:41 PM, Sam W wrote:
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Thanks Doug, I'll try that. How would you register the lesion image (which is
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Thanks Doug, I'll try that. How would you register the lesion image (which
is anatomical space) to orig.mgz? I thought this would work:
mri_coreg --mov /data/sub01/anat.nii.gz --targ orig.mgz --reg
/data/sub01/reg.lta
mri_vol2vol --mov
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
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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
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
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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
