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ENH: run a second ``N4BiasFieldCorrection`` node to refine INU correction #342

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merged 2 commits into from Apr 23, 2019

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commented Apr 22, 2019

An additional INU correction step is included to run on the original
images (without truncating). Two further improvements are also being added:

  1. if ATROPOS was run (atropos_refine == True), the WM tissue probability map is used
  2. the N4 algorithm is configured with 5 iterations instead of 4 for a
    more homogeneous white matter (close poldracklab/smriprep#38).

This PR may help alleviate the problem in poldracklab/smriprep#19, and
https://neurostars.org/t/fmriprep-t1-surface-issues/4089

oesteban added some commits Apr 22, 2019

enh(workflows): run a second ``N4BiasFieldCorrection`` node on the or…
…iginal image

An additional INU correction step is included to run on the original
images (without truncating). Two further improvements are also being added:
1. if ATROPOS was run (``atropos_refine == True``), the WM tissue probability map is used
2. the N4 algorithm is configured with 5 iterations instead of 4 for a
more homogeneous white matter (close poldracklab/smriprep#38).

This PR may help alleviate the problem in poldracklab/smriprep#19, and
https://neurostars.org/t/fmriprep-t1-surface-issues/4089

@oesteban oesteban merged commit f3da667 into poldracklab:master Apr 23, 2019

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Codacy/PR Quality Review Up to standards. A positive pull request.
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@oesteban oesteban deleted the oesteban:enh/revise-n4 branch Apr 23, 2019

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