FieldTrip

We try to develop FieldTrip in such a way that it works with the latest MATLAB release on the most popular operating system platforms, but at the same time we try to have it work with as many older MATLAB versions as possible. However, the MATLAB syntax and the availability of functions in the standard Mathworks toolboxes changes over time. Consequently, sometimes we will use MATLAB code that is only supported from a certain version upwards.

An online poll in April 2011 showed that a large quantity of our users access the FieldTrip toolbox with a Matlab version younger than 2006 (<5 years). The full results can be found here.

MATLAB includes a large number of functions in standard toolboxes that come with every installation, but certain functions are included in additional (commercial) toolboxes from Mathworks, such as the signal processing or the statistics toolbox. Whether you need to buy these toolboxes depends on whether you want to use specific functionality in FieldTrip. We try to avoid using these additional Mathworks toolboxes to the extent that we will look for alternatives (e.g. from Octave) or use drop-in replacement functions for certain functions, as long as the time required to implement these alternatives is not too large. The Mathworks toolboxes that some of the FieldTrip functions (main functions listed) currently make use of (or can make use of) are

• Signal processing toolbox
  1. ft_mvaranalysis (dpss.m, window.m)
  2. ft_resampledata (resample.m)
  3. ft_spike_triggeredspectrum and ft_spiketriggeredspectrum (dpss.m, window.m)
  4. ft_spikeanalysis (hilbert.m)
  5. ft_preproc_bandpassfilter (fir1.m)
  6. ft_preproc_bandstopfilter (fir1.m)
  7. ft_preproc_denoise (hilbert.m)
  8. ft_preproc_highpassfilter (fir1.m)
  9. ft_preproc_hilbert (hilbert.m)
  10. ft_preproc_lowpassfilter (fir1.m)
  11. ft_preproc_medianfilter (medfilt1.m)
  12. ft_preproc_resample (decimate.m, downsample.m, resample.m)
  13. ft_specest_hilbert (hilbert.m)
  14. ft_specest_mtmconvol (dpss.m, window.m)
  15. ft_specest_mtmfft (dpss.m, window.m)
  16. trialfun_example2 (hilbert.m)

• Statistics toolbox (used for channel- and source-level cluster statistics)
  1. ft_connectivitysimulation (mvnrnd.m)
  2. ft_headmovement (kmeans.m)
  3. ft_qualitycheck (boxplot.m)
  4. ft_sourcedescriptives (kurtosis.m)
  5. ft_spike_isihist (mle.m)
  6. ft_spike_plot_isi (gampdf.m)
  7. ft_spike_plot_isireturn (mvnpdf.m)
  8. ft_spike_plot_jpsth (mvnpdf.m)
  9. ft_spikesorting (kmeans.m)
  10. ft_stratify (linkage.m, pdist.m, squareform.m)
  11. statistics_stats (anova1.m, kruskalwallis.m, ttest.m, ttest2.m)
  12. ft_connectivity_ppc (nansum.m)
  13. ft_connectivity_wpli (nansum.m)
  14. statfun_depsamplesF (fcdf.m, finv.m)
  15. statfun_indepsamplesF (fcdf.m, finv.m)
  16. statfun_indepsampleszcoh (normcdf.m, norminv.m)

• Optimization toolbox (used only for dipole fitting)
  1. dipole_fit (fminunc.m)
  2. warp_optim (fminunc.m)

• Image processing toolbox
  1. ft_layoutplot (imread.m)
  2. ft_prepare_layout (imread.m)
  3. ft_sourceplot (imfill.m)
  4. ft_volumesegment (imdilate.m)
  5. ft_read_mri (dicominfo.m, dicomread.m)

To prevent unnecessary dependencies on functions from additional Mathworks toolboxes, FieldTrip includes a number of drop-in replacement functions with the same behaviour as their Matlab counterpart. These functions are located in fieldtrip/private and include

• nansum, nanstd
• biocdf, binopdf
• tcdf
• range

complete the list of drop-in replacement functions.