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‎.zenodo.json

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{
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"creators": [
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{
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"affiliation": "Department of Psychology, Stanford University",
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"name": "Gorgolewski, Krzysztof J.",
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"orcid": "0000-0003-3321-7583"
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},
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{
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"affiliation": "Department of Psychology, Stanford University",
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"name": "Esteban, Oscar",
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"orcid": "0000-0001-8435-6191"
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},
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{
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"name": "Burns, Christopher"
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{
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"affiliation": "Independent",
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"name": "Ziegler, Erik",
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"orcid": "0000-0003-1857-8129"
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},
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{
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"name": "Pinsard, Basile"
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},
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{
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"name": "Madison, Cindee"
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},
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{
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"affiliation": "Department of Psychology, Stanford University",
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"name": "Waskom, Michael"
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},
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{
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"affiliation": "The University of Iowa",
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"name": "Ellis, David Gage",
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"orcid": "0000-0002-3718-6836"
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},
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{
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"affiliation": "UC Berkeley",
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"name": "Clark, Dav",
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"orcid": "0000-0002-3982-4416"
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},
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{
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"affiliation": "Mayo Clinic, Neurology, Rochester, MN, USA",
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"name": "Dayan, Michael",
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"orcid": "0000-0002-2666-0969"
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},
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{
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"affiliation": "Klinikum rechts der Isar, TUM. ACPySS",
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"name": "Manh\u00e3es-Savio, Alexandre",
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"orcid": "0000-0002-6608-6885"
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},
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{
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"affiliation": "The Laboratory for Investigative Neurophysiology (The LINE), Department of Radiology and Department of Clinical Neurosciences, Lausanne, Switzerland; Center for Biomedical Imaging (CIBM), Lausanne, Switzerland",
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"name": "Notter, Michael Philipp",
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"orcid": "0000-0002-5866-047X"
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},
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{
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"affiliation": "University of Iowa",
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"name": "Johnson, Hans",
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"orcid": "0000-0001-9513-2660"
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},
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{
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"affiliation": "Department of Electrical and Computer Engineering, Johns Hopkins University",
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"name": "Dewey, Blake E",
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},
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{
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"affiliation": "Dartmouth College: Hanover, NH, United States",
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"name": "Halchenko, Yaroslav O.",
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"orcid": "0000-0003-3456-2493"
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},
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{
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"name": "Hamalainen, Carlo",
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{
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"affiliation": "UC Berkeley - UCSF Graduate Program in Bioengineering",
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"name": "Keshavan, Anisha",
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},
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{
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"affiliation": "Developer",
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},
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{
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"affiliation": "Research Group Neuroanatomy and Connectivity, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany",
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{
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"affiliation": "Otto-von-Guericke-University Magdeburg, Germany",
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{
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"name": "Wassermann , Demian",
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},
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{
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"affiliation": "University College London",
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},
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{
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"affiliation": "Boston University",
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{
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},
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{
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"affiliation": "Washington University in St Louis",
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{
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"name": "Forbes, Jessica"
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{
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},
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{
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"affiliation": "State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China; Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands",
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"name": "Kong, Xiang-Zhen",
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},
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{
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"affiliation": "CNRS LTCI, Telecom ParisTech, Universit\u00e9 Paris-Saclay",
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{
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"affiliation": "UniversityHospital Heidelberg, Germany",
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"name": "Kleesiek, Jens"
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{
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"name": "Schaefer, Alexander",
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},
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{
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"affiliation": "Nathan s Kline institute for psychiatric research",
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"name": "Sikka, Sharad"
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},
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{
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"affiliation": "Neurospin/Unicog/Inserm/CEA",
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"name": "Perez-Guevara, Martin Felipe",
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},
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{
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"affiliation": "1 McGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montr\u00e9al, 3801 University Street, WB-208, H3A 2B4, Qu\u00e9bec, Canada. 2 University of Lyon, CNRS, INSERM, CREATIS., Villeurbanne, 7, avenue Jean Capelle, 69621, France.",
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"name": "Glatard, Tristan",
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},
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{
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"affiliation": "Duke University",
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"name": "Iqbal, Shariq",
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},
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{
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"affiliation": "The University of Sydney",
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"name": "Liu, Siqi"
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},
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{
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"affiliation": "University of Iowa",
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"name": "Welch, David"
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},
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{
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"affiliation": "University of illinois urbana champaign",
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"name": "Sharp, Paul"
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},
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{
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"affiliation": "Mayo Clinic",
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"name": "Warner, Joshua",
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},
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{
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"affiliation": "Harvard University - Psychology",
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"name": "Kastman, Erik",
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"orcid": "0000-0001-7221-9042"
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},
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{
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"affiliation": "MPI CBS Leipzig, Germany",
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"name": "Lampe, Leonie"
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},
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{
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"affiliation": "Boston University",
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"name": "Perkins, L. Nathan"
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},
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{
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"affiliation": "Child Mind Institite",
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"name": "Craddock, R. Cameron",
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{
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"name": "K\u00fcttner, Ren\u00e9"
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"name": "Bielievtsov, Dmytro",
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},
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{
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"affiliation": "Technische Universit\u00e4t Dresden, Faculty of Medicine, Department of Child and Adolescent Psychiatry",
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"name": "Geisler, Daniel",
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},
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{
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"affiliation": "Institute of Neuroinformatics, ETH/University of Zurich",
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"name": "Gerhard, Stephan",
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{
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"affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany",
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"name": "Liem, Franziskus",
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},
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{
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"affiliation": "German Institute for International Educational Research",
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"name": "Linkersd\u00f6rfer, Janosch",
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},
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{
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"affiliation": "Max Planck Research Group for Neuroanatomy & Connectivity, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany",
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"name": "Margulies, Daniel S.",
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},
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{
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"affiliation": "University of Helsinki",
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"name": "Andberg, Sami Kristian",
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"orcid": "0000-0002-5650-3964"
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},
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{
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"affiliation": "Leibniz Institute for Neurobiology",
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"name": "Stadler, J\u00f6rg",
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"orcid": "0000-0003-4313-129X"
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},
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{
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"affiliation": "MPI-CBS; McGill University",
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"name": "Steele, Christopher John",
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"orcid": "0000-0003-1656-7928"
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},
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{
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"affiliation": "Duke University",
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"name": "Broderick, William",
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"orcid": "0000-0002-8999-9003"
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},
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{
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"affiliation": "UC San Diego",
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"name": "Cipollini, Ben",
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"orcid": "0000-0002-7782-0790"
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},
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{
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"affiliation": "University of Newcastle, Australia",
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"name": "Cooper, Gavin",
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"orcid": "0000-0002-7186-5293"
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},
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{
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"affiliation": "The University of Texas at Austin",
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"name": "Floren, Andrew",
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"orcid": "0000-0003-3618-2056"
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},
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{
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"affiliation": "State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China",
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"name": "Huang, Lijie",
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"orcid": "0000-0002-9910-5069"
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},
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{
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"affiliation": "Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA",
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"name": "Gonzalez, Ivan",
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"orcid": "0000-0002-6451-6909"
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},
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{
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"affiliation": "University of Cambridge",
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"name": "McNamee, Daniel",
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"orcid": "0000-0001-9928-4960"
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},
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{
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"affiliation": "CEA",
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"name": "Papadopoulos Orfanos, Dimitri",
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{
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"affiliation": "Child Mind Institute / Nathan Kline Institute",
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"name": "Pellman, John",
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"orcid": "0000-0001-6810-4461"
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},
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{
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"affiliation": "Department of Psychology, Stanford University",
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"name": "Triplett, William",
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"orcid": "0000-0002-9546-1306"
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},
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{
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"affiliation": "MIT, HMS",
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"name": "Ghosh, Satrajit",
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"orcid": "0000-0002-5312-6729"
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}
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],
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"keywords": [
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"neuroimaging",
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"workflow",
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"pipeline"
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],
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"license": "Apache-2.0",
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"related_identifiers": [
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{
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"identifier": "https://github.com/nipy/nipype/tree/0.12.0-rc1",
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"relation": "isSupplementTo",
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"scheme": "url"
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},
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{
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"identifier": "10.3389/fninf.2011.00013",
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"relation": "isNewVersionOf",
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"scheme": "doi"
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}
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],
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"upload_type": "software"
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}

‎CONTRIBUTING.md

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* adding more information about what may have caused the error.
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Raise a new exception using ``raise_from(NewException("message"), oldException)`` from ``future``.
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Do not log this, as it creates redundant/confusing logs.
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* If you are new to the project don't forget to add your name and affiliation to the `.zenodo.json` file.
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## Contributing issues
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‎doc/about.rst

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url = {http://dx.doi.org/10.5281/zenodo.50186}
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}
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If you are a Nipype contributor and your name is not mentioned above please submit
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a Pull Request modifying `.zenodo.json` file.
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When publishing results obtained using Nipype we strongly encourage citing the above reference to give credit to all
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Nipype contributors. However, if for some reason the journal you are publishing with does not allow you do cite software
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this way you can use the initial paper published in 2011 (see below).

‎nipype/interfaces/freesurfer/preprocess.py

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desc="force use of nifti rather than analyze with SPM")
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epi_mask = traits.Bool(argstr="--epi-mask",
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desc="mask out B0 regions in stages 1 and 2")
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dof = traits.Enum(6, 9, 12, argstr='--%d',
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desc='number of transform degrees of freedom')
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fsldof = traits.Int(argstr='--fsl-dof %d',
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desc='degrees of freedom for initial registration (FSL)')
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out_fsl_file = traits.Either(traits.Bool, File, argstr="--fslmat %s",
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desc="write the transformation matrix in FSL FLIRT format")
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registered_file = traits.Either(traits.Bool, File, argstr='--o %s',
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"""Use FreeSurfer bbregister to register a volume to the Freesurfer anatomical.
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This program performs within-subject, cross-modal registration using a
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boundary-based cost function. The registration is constrained to be 6
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DOF (rigid). It is required that you have an anatomical scan of the
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subject that has already been recon-all-ed using freesurfer.
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boundary-based cost function. It is required that you have an anatomical
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scan of the subject that has already been recon-all-ed using freesurfer.
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Examples
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--------

‎nipype/interfaces/freesurfer/tests/test_BBRegister.py

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input_map_5_3 = dict(
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args=dict(argstr='%s',),
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contrast_type=dict(argstr='--%s', mandatory=True,),
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dof=dict(argstr='--%d',),
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environ=dict(nohash=True, usedefault=True,),
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epi_mask=dict(argstr='--epi-mask',),
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fsldof=dict(argstr='--fsl-dof %d',),
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ignore_exception=dict(nohash=True, usedefault=True,),
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init=dict(argstr='--init-%s', mandatory=True, xor=['init_reg_file'],),
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init_reg_file=dict(argstr='--init-reg %s', mandatory=True, xor=['init'],),
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input_map_6_0 = dict(
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args=dict(argstr='%s',),
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contrast_type=dict(argstr='--%s', mandatory=True,),
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dof=dict(argstr='--%d',),
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environ=dict(nohash=True, usedefault=True,),
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epi_mask=dict(argstr='--epi-mask',),
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fsldof=dict(argstr='--fsl-dof %d',),
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ignore_exception=dict(nohash=True, usedefault=True,),
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init=dict(argstr='--init-%s', xor=['init_reg_file'],),
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init_reg_file=dict(argstr='--init-reg %s', xor=['init'],),

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