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Add 3dDespike step #699

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chrisgorgo opened this issue Sep 12, 2017 · 3 comments

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@chrisgorgo
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commented Sep 12, 2017

https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dDespike.html

  • motion estimation should be done on data that was not despiked
  • use the -NEW method
  • try to use multiple threads
  • pass in the ignore option from non-steady state detector

@chrisgorgo chrisgorgo added the feature label Sep 12, 2017

@oesteban oesteban modified the milestones: 1.0.0-rc4, Future Sep 12, 2017

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commented Sep 12, 2017

Interesting and related resources are this blog post that Chris shared some days ago, and J. Power's recent paper: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0182939

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commented Sep 20, 2017

piggybacking off @oesteban's resources, if you haven't already seen it, the Satterthwaite group released a paper in July about bench-marking different confound combinations for functional connectivity analyses, including despiking and censoring: http://www.sciencedirect.com/science/article/pii/S1053811917302288?via%3Dihub

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commented Sep 20, 2017

@oesteban oesteban added this to To do in pipelines via automation Jul 9, 2019

@oesteban oesteban removed this from the Future milestone Jul 9, 2019

@franklin-feingold franklin-feingold moved this from To do to Issues C-list in pipelines Jul 10, 2019

@oesteban oesteban added this to the 2.0.0 milestone Jul 11, 2019

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