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N4BiasFieldCorrection only honors --rescale-intensities when a mask image (-x) is provided; without one the flag is silently ignored. Every caller that set rescale_intensities now also wires an existing upstream brain mask into mask_image so the rescale is applied, as antsAtroposN4.sh does for its N4 step (-x mask, -w weights): - init_brain_extraction_wf: the warped, thresholded template brain mask - init_atropos_wf: the refined brain mask (msk_conform output) - init_n4_only_wf: the binarized input mask - init_enhance_and_skullstrip_bold_wf: the tentative brain mask that already feeds weight_image afni_wf runs N4 before skull-stripping, so no mask exists there; the dead option is removed rather than left misleadingly set. Fixes nipreps#1054.
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Title:
FIX: Pass a mask image to N4 so --rescale-intensities takes effect