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Difference between -o and -s ? #37

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tashrifbillah opened this issue Sep 22, 2022 · 5 comments
Open

Difference between -o and -s ? #37

tashrifbillah opened this issue Sep 22, 2022 · 5 comments

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@tashrifbillah
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tashrifbillah commented Sep 22, 2022

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

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

@tashrifbillah
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It did not!

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

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