ANTsX
surface normal (vector) in cortical thickness analysis
ANTs developers,
Is there any way to get surface normal (3D vector indicating the correspondence from WM point to GM point)f for gray matter voxels like FreeSurfer?
In the same way, can we apply the cortical thickness pipeline to analyze the thickness of subdural space (CSF space between the skull and outer GM) ?
Thank you.
Jeongchul.
Is there any way to get surface normal (3D vector indicating the correspondence from WM point to GM point)f for gray matter voxels like FreeSurfer?
You can probably get that functionality from VTK. We have a number of tools which interface with VTK (e.g., antsSurf) but nothing specifically for normals like FreeSurfer.
In the same way, can we apply the cortical thickness pipeline to analyze the thickness of subdural space (CSF space between the skull and outer GM) ?
Yes, you can apply KellyKapowski to that problem. However, parameter selection is tricky---you wouldn't want to simply apply what's in antsCorticalThickness.sh to that problem.
the "surface" in kellykapowski is treated probabilistically.
its normal direction is determined by the gradient of the probability map and thus is also probabilistic.
brian
On Wed, Mar 6, 2019 at 2:37 PM Nick Tustison [email protected] wrote:
Is there any way to get surface normal (3D vector indicating the correspondence from WM point to GM point)f for gray matter voxels like FreeSurfer?
You can probably get that functionality from VTK. We have a number of tools which interface with VTK (e.g., antsSurf) but nothing specifically for normals like FreeSurfer.
In the same way, can we apply the cortical thickness pipeline to analyze the thickness of subdural space (CSF space between the skull and outer GM) ?
Yes, you can apply KellyKapowski to that problem. However, parameter selection is tricky---you wouldn't want to simply apply what's in antsCorticalThickness.sh to that problem.
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Brian, It seems the option writing the surface normal is not available in kellykapowski. Then, is it reasonable to estimate the surface normal from the GM probability map (output of antsCorticalThickness.sh) using some matlab functions to estimate the gradient of the image (i.e. imgradientxyz or 3D Gradient Vector Flow (GVF3))? Thank you.
Jeongchul.