Difference between -o and -s ?

[tashrifbillah]

Folks, can you remind us the difference between -o as a file and -s? I used:

hd-bet -i T1w.nii.gz -o mask.nii.gz

but got two files:

mask.nii.gz and mask_mask.nii.gz

Do I need:

hd-bet -i T1w.nii.gz -o mask.nii.gz -s 0

Your documentation is unclear on this.

[FabianIsensee]

-o is the output image (your input image with everything that is not brain set to 0) -s is the segmentation mask of the brain, so it's 1 wherever the model thinks the brain is

[tashrifbillah]

Yes, I figured them out through experiement. I'll try to add them to your README.md and submit a PR.

[FabianIsensee]

have you tried hd-bet -h? That should tell you all this as well ;-)

[tashrifbillah]

It did not!

[FabianIsensee]

I see :-) If you want to make a PR clarifying this I am happy to accept it :-)