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NeuroElf wiki

NeuroElf logoWelcome to the NeuroElf wiki. If you would like to contribute, please read the information provided in the wiki internals section below, email register (at) neuroelf (dot) info, and once you get your user information, you can edit/add articles! :)

Below you can find a preliminary and manually maintained table of contents. This means that in case you create a new article when you write up your own piece of documentation, please name it with a useful title, and if you consider the information you provide to be useful in a global context (e.g. a manual on how to use a specific tool or a solution to a general problem), please add the article to this page.

Once there is a sufficiently large number of articles, this will be re-organized, but for now, this should be good enough to quickly find the required information (given it is available here on the wiki).

Please note: manuals available here at the wiki mostly reflect the most up-to-date version of files available in the daily snapshot (see the main page for the link)! If a feature described therein isn't part of that last stable release, please (temporarily) use the snapshot release, if you need this feature urgently!


wiki internals

Matlab basics

NeuroElf internals

Data analysis - step-by-step suggestions/instructions for a processing stream

User's corner

Graphical User Interface (GUI)

How-to... guides

Class overview





Function reference

This section is sorted by area of application. To look up help for a specific function name, please use the Search box on top of any wiki page or look at the alphabetical function index.

BrainVoyager specific

  • averagevmrs - average multiple VMRs into one dataset
  • bcc2area - lookup labels of color codes used in BrainVoyager QX's Talairach.VMR
  • createfmr - create a BrainVoyager compatible FMR object from DICOM, PAR/REC, or Analyze files
  • createvmr - create a BrainVoyager compatible VMR object from DICOM, PAR/REC, or Analyze file(s)
  • vmrspmcoreg - apply SPM's coregistration to two VMRs and create a TRF object

Data import

Fun functions

  • solvesudoku - Sudoku puzzle solver (not the best one, but it works)

Information processing

  • acsvread - read CSV (comma-separated-value) files (e.g. text-based Excel sheets)
  • findfiles - seek file/folder names in filesystem, create list of filenames with pattern for scripted processing
  • qsort - C-based Qsort algorithm (only for certain applications
  • u8str2double - parsing large text files with tabular numeric data (MEX file: fast)

Interpolation (resampling)

Physiological data processing

  • computehrv - compute heart-rate variability (HRV) from onset data
  • heartbeats - detect and visualize heart beats from ECG recording (incl. manual de/selection of problematic beat locations)
  • plotcurves - flexibly visualize curves and, if requested, determine points of interest (e.g. peaks) and compute distances (response times, amplitudes, etc.)
  • prefilter - pre-processing filter of signal data (removal of unwanted frequencies, resonance, and noise components)

Robust regression

  • fitrobustbisquare - robustly fit (weighted) least-squares model by iteratively re-weighting outliers using the bisquare function
  • fitrobustbisquare_img - apply robust fit on multi-dimensional data, instance-by-instance (faster than looping around fitrobustbisquare)

Spatial data processing

Spatial transformations (incl. coordinates)


  • alphasim - simulate random data/maps to determine cluster level threshold under given smoothing conditions
  • calcbetas - perform ordinary least-squares (OLS) regression and, if requested, compute predicted time course and SE
  • conjval and conjvalp - compute conjunction of statistics (where conjvalp inverts the min to a max logic for signed, one-tailed p-values)
  • correlinvtstat, correlpvalue, and correltstat - convert correlation coefficient ® from/into t-statistic (or p-value)
  • corrmap - correlation map with support for OLS, robust regression, and Kendall Tau coefficient
  • cov_nd - compute covariance/correlation arrays over last dimension of N-dimensional data
  • custom_pwelch - compute Welch's method periodogram over data
  • kurt - kurtosis
  • sdist - statistical distributions (one function, e.g. Fcdf, tcdf, tinv, etc.)
  • skew - skewness
  • varc - C-based variance (faster for single-core processing)

Temporal transformations

  • psctrans - per cent signal change (%) transformation (incl. applying transform in one dimension for multi-dimensional data)
  • tempfilter - apply temporal filtering to (multi-dimensional) data
  • ztrans - z-transformation (incl. applying transform in one dimension for multi-dimensional data)

User Interface (UI) functions

  • colorpicker - select color(s) from RGB/HSV color space

Auxiliary functions

Dealing with errors

start.txt · Last modified: 2016/05/27 15:19 by jochen