% IMPORTANT: The following is UTF-8 encoded.  This means that in the presence
% of non-ASCII characters, it will not work with BibTeX 0.99 or older.
% Instead, you should use an up-to-date BibTeX implementation like “bibtex8” or
% “biber”.

@PHDTHESIS{Reuter:916043,
      author       = {Reuter, Niels},
      title        = {{P}ainting the {B}rain by {N}umbers: {I}ntroducing an
                      open-source approach to automated regional
                      connectivity-based parcellation},
      school       = {Heinrich Heine Universitat Dusseldorf},
      type         = {Dissertation},
      reportid     = {FZJ-2022-05889},
      pages        = {161 p.},
      year         = {2022},
      note         = {Grants that are not listed: - Deutsche
                      Forschungsgemeinschaft (DFG, EI 816/11-1) - National
                      Institute of Mental Health (R01-MH074457) - The Helmholtz
                      Portfolio Theme "Supercomputing and Modelling for the Human
                      Brain"Selecting a POF topic appears to be mandatory, but my
                      work was done under the previous POF period.; Dissertation,
                      Heinrich Heine Universitat Dusseldorf, 2022},
      abstract     = {Regional connectivity-based parcellation (rCBP) is a widely
                      used procedure for investigating the structural and
                      functional differentiation within a region-of-interest (ROI)
                      based on its long-range connectivity. No standardized
                      software or guidelines currently exist for applying rCBP,
                      making the method only accessible to those who develop their
                      own tools. A historical background to rCBP has been provided
                      in chapter 1, which continues with the aim of this work:
                      introducing CBPtools, an open-source software package
                      implementing rCBP. The chapter concludes by detailing
                      various methods and concepts associated with the rCBP
                      procedure.CBPtools is a Python (version 3.5+) package that
                      allows users to run an extensively evaluated rCBP analysis
                      workflow on a given ROI. It currently supports two
                      modalities: resting-state functional connectivity and
                      structural connectivity based on diffusion-weighted imaging,
                      along with support for custom connectivity matrices.
                      Analysis parameters are customizable, and the workflow can
                      be scaled to many subjects using a parallel processing
                      environment. Parcellation results with corresponding
                      validity metrics are provided as textual and graphical
                      output. Thus, CBPtools provides a simple plug-and-play yet
                      customizable way to conduct rCBP analyses. Chapter two
                      discusses architectural choices, scope, and software
                      dependencies, followed by a thorough description of all
                      implemented features as well as a step-by-step guide through
                      the processing pipeline.In chapter three we demonstrate the
                      utility of CBPtools using a voluminous data set on an
                      average compute-cluster infrastructure by performing rCBP on
                      three ROIs prominently featured in parcellation literature.
                      A side-project on the investigation of potential issues
                      regarding outliers in the data set is added as chapter
                      four.In closing we discuss our findings, provide
                      recommendations, and suggest future extensions to the
                      CBPtools software in chapters five and six. CBPtools is
                      capable of reproducing parcellations found in existing
                      literature. It offers flexibility in terms of customization
                      while remaining easy to use. By providing an open-source
                      software we aim to promote reproducible and comparable rCBP
                      analyses and, importantly, make the rCBP procedure readily
                      available.},
      cin          = {INM-7},
      cid          = {I:(DE-Juel1)INM-7-20090406},
      pnm          = {5235 - Digitization of Neuroscience and User-Community
                      Building (POF4-523) / 5251 - Multilevel Brain Organization
                      and Variability (POF4-525) / HBP SGA2 - Human Brain Project
                      Specific Grant Agreement 2 (785907)},
      pid          = {G:(DE-HGF)POF4-5235 / G:(DE-HGF)POF4-5251 /
                      G:(EU-Grant)785907},
      typ          = {PUB:(DE-HGF)11},
      url          = {https://juser.fz-juelich.de/record/916043},
}