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Input files and structures

Accepted file extensions

  • Text files (.txt)
  • Tab-separated files (.tsv)
  • Generic data files (.dat)
  • Numpy array (.npy)
  • MATLAB (.mat) files (v4 and v6-7.2 using scipy.io.loadmat, v7.3 using mat73 package)
  • HDF5 (.h5) files
  • zip folders containing all above file extensions

Required and recommended fields

Please note the following rules and recommendations:

  • The most important file to have for conversions is Structural Connectome which is must be named weights.
  • Recommended files:
    • centres (or nodes and labels separately),
    • distances (or tract_lengths which is the other name for distances, thus this file will be renamed to distances both in the input and output folders)
    • Python, MATLAB or R code that can reproduce the results
    • empirical and simulated time series and time stamps.
  • average_orientation or orientation will be renamed to normals according to BEP034 both in the input and output folders.

Accepted files

Here is the list of files that are supported by the app categorized by their respective folders.

Coordinates (coord folder)
File name Description Dimensions Notes
centres consists of nodes (nx1 vector) and labels (nx3 matrix) in that order. nx4 See description of nodes and labels below
nodes These are the region labels (e.g., lh_bankssts, lh_superiorfrontal). nx1 recommended
delays These are the 3d coordinate centres nx3 recommended
times These are the time steps of the simulated time series. nx1 recommended
bold_times These are the time steps of the simulated BOLD time series. nx1 recommended
areas This is the estimated vector each region's area in mm^2. nx1 optional
cortical This is the vector that distinguishes cortical (1) from subcortical (0) regions. nx1 optional
average orientations, normals normals. nx3 optional. If the file name is average_orientation, it will be named normals in input and output folders.
hemisphere The vector that distinguishes right (1) from left (0) hemisphere. nx1 optional.
faces These are the faces of cortex surface triangulation.   optional.
vertices These are the vertices of cortex surface triangulation.   optional.
map This is the nxm matrix where the coordinates along rows are mapped to the coordinates along columns. nxm optional.