Dear Yang Hu,
On Mon, 10 Jun 2019 16:26:47 +0800, huyang <[log in to unmask]> wrote:
>Dear CAT12 experts,
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>(1) I found that CAT12 provides several skull-stripping methods but could not produce skull-stripped results (i.e., brain). Is there an option to output skull-stripped results? Or could we use the partial volume label image (p0*) as a brain mask?
You can use the p0 label image with spm imcalc to obtain a skull-stripped T1 image in native space.
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>(2) In the partial volume label image, there are numbers (for instance, 1.53) at the range of 1-2 or 2-3 ( 1/2/3 represent different tissue types), what these numbers represent? If I want to get a hard tissue segmentation results (i.e., binary segmentation), how should I best threshold the partial volume estimation maps (p0/p1/p2/p3)?
The label image is based on partial volume estimation and the fuzzy values are used to define the partial volume. In order to get a hard tissue segmentation you can simply use the round function in imcalc.
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>(3) In the 12.6+ version, the report PDF would overlay a skull and brain contour above the original T1 image. My question is that what the skull and brain contour represents? It is the skull and brain contour of the TPM.nii for checking affine registration, Or it is the contour from the final results for checking partial volume estimation?
It's the skull and brain contour of the TPM to check the quality of the initial affine registration.
Best,
Christian
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>Many thanks!
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>Best,
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>Yang Hu
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