Many of the functions for general fMRI preprocessing are wrappers for existing well-established neuroimaging tools. The wrappers should be seen as a consistent MATLAB command line interface to these functions, not as a reimplementation. A large part of these functions are written for my own convenience. A substantial part is new method development, mainly regarding laminar analysis.

• From this project root, run tvm_installLaminarAnalysisToolbox.m in MATLAB
• SPM needs to be in your MATLAB path (used throughout the toolbox)
• FreeSurfer and dcm2nii are used sporadically.
  • dcm2nii needs to be in the .profile if you want to convert dicoms to niftis
  • FreeSurfer needs to be installed and the setup needs to be in the .profile
  • At some point with some MATLAB versions, the following line needed to be added to your .bashrc:
    • export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH

All functions that are part of the main pipeline can be found in the Interface section of the toolbox and all adhere to the same structure. Every function takes a single configuration structure as input. It does not generate output to the MATLAB workspace, but instead writes output to designated files as listed in the configuration. As an example:

cfg = [];
cfg.i_SubjectDirectory = ...;
cfg.i_ReferenceVolume = ...;
cfg.o_OutputFile = ...;
tvm_someFunction(cfg);

Fields that represent input files and parameters start with an i_, output fields start with an o_. Most functions have the option of a i_SubjectDirectory, being the root directory to which the input and output files are relative. It defaults to the current working directory. All interface functions are added to the Graphical User Interface Porcupine.

Copyright (C) 2013-2017, Tim van Mourik, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands DCCN