Hi John,
Just take the grey matter pve output (usually *_pve_1.nii.gz from a standard T1-weighted image) and use fslmaths to threshold and binarise it.
That is:
fslmaths image_pve_1.nii.gz -thr 0.2 -bin gm_mask
where "image_pve_1.nii.gz" should be the name of _your_ specific grey matter pve image from FAST.
All the best,
Mark
> On 28 Sep 2018, at 19:31, John Guige <[log in to unmask]> wrote:
>
> Hello everyone,
> I hope you are well. Currently, I am trying to find out how to make a grey matter mask with FAST. I know mostly how to make the map, but I need to set the probability threshold for the Grey Matter at above 20%, so that in the binary segmentation, the grey matter is only presented as 1 if there is a 20% chance or more that the tissue is grey matter in the MNI template. I hope that makes sense. Any help on this would be great!
>
> Thank you!
>
> John
>
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