Dear Eleni,
I would try a lower threshold of 0.1 as recommended. Furthermore, the large missing areas might be due to GM areas with zeros in your images or failed skull-stripping )although it looks a lot worse). Thus, I would check your data for large areas where tissue is missing.
Best,
Christian
On Mon, 7 Jun 2021 13:39:22 +0100, Eleni Panagoulas <[log in to unmask]> wrote:
>Dear SPM and CAT12 experts,
>
> I am currently running a VBM analysis and using a 0.2 absolute threshold mask during statistical analysis. However, when I look at the mask.nii file it seems that a lot of grey matter and the right thalamus are missing from the mask. I have attached a screenshot above.I am fairly new to VBM and I was wondering why could this be happening? When I create a mean mask of all normalized grey matter images and then threshold it to 0.2 the mask looks more normal. I appreciate your help.
>
>Best wishes,
>Eleni
>
>
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