re-apply mask to brainchop result to avoid negative values#1
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kjamison wants to merge 1 commit intorordenlab:mainfrom
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re-apply mask to brainchop result to avoid negative values#1kjamison wants to merge 1 commit intorordenlab:mainfrom
kjamison wants to merge 1 commit intorordenlab:mainfrom
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…k to do_brainchop() to load the binary mask and remask the output, and use this by default in normalize()
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brainchop sometimes gives negative values outside mask, which then causes ANTs registration to fail. This PR adds apply_mask to do_brainchop(), which runs brainchop with additional
-a maskfile.nii.gz, and then loads that binary mask to remask thebt1output. By default, normalize() uses this new do_brainchop(apply_mask=True) option