ENH: reference workflow N4 improvements #40
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this will be added as a second PR
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Changes proposed in this pull request
This makes the rodent-specific arguments (made available by nipreps/niworkflows#630) available to the reference workflow for more robust N4 correction. This should make the reference image easier to mask.
Also worth noting that in this scenario, brain extraction is run only once (on the structural image), and the registration between structural and functional is run without masking.
Also updatedFLIRTRPTto include--basescale 1argument, based on the conversation had over at nipreps/fmriprep#2624, to overcome problems in coregistration when testing locally.EDIT: this has been removed and will be added to a separate PR
Documentation that should be reviewed