Hi
I think you can simply use the vertex-wise distance between the inskull and outskull meshes (vtk files).
To extract the vertex coordinates from the vtk files you can for example do this in a shell:
n=`cat sub-01_T1w.nii_bet_inskull_mesh.vtk | grep POINTS | awk ‘{print $2}’`
cat sub-01_T1w.nii_bet_inskull_mesh.vtk | grep -A $n | tail -n $n > inskull.txt
cat sub-01_T1w.nii_bet_outskull_mesh.vtk | grep -A $n | tail -n $n > outskull.txt
The two text files inskull.txt and outskull.txt contain vertex coordinates. You can calculate the vertexwise distances easily with some data analysis tool, e.g. in matlab:
inskull = load(‘inskull.txt’);
outskull = load(‘outskull.txt’);
dist = sqrt(sum((inskull-outskull).^2,2));
Cheers
Saad
> On 15 Aug 2019, at 08:54, Xuesong Le <[log in to unmask]> wrote:
>
> Hi, All.
> I am taking a brain imaging project. One of the early steps requires measuring the thickness of skull from MRI image.
> As guided by the BET manual, "A This runs both bet2 and betsurf programs in order to get the additional skull and scalp surfaces created by betsurf."
>
> Given T1 weighted file 'sub-01_T1w.nii.gz' as an input, 'bet sub-01_T1w.nii.gz sub-01_T1w.nii_bet.nii.gz -R -m -A' command generates
> following files:
>
> sub-01_T1w_bet_outskull_mesh.nii.gz
> sub-01_T1w_bet_inskull_mask.nii.gz sub-01_T1w_bet_skull_mask.nii.gz
> sub-01_T1w_bet_inskull_mesh.nii.gz sub-01_T1w.nii_bet_inskull_mesh.vtk
> sub-01_T1w_bet_mask.nii.gz sub-01_T1w.nii_bet_mesh.vtk
> sub-01_T1w_bet.nii.gz sub-01_T1w.nii_bet_outskin_mesh.vtk
> sub-01_T1w_bet_outskin_mask.nii.gz sub-01_T1w.nii_bet_outskull_mesh.vtk
> sub-01_T1w_bet_outskin_mesh.nii.gz sub-01_T1w.nii.gz
> sub-01_T1w_bet_outskull_mask.nii.gz
>
> But I am not sure how to measure the thickness of skull by using those files. Would you be able to shed some light on this? Sorry, I am new to this area.
>
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