2010-02-17 15:58 roboos * private: added provate directory with replacement function for butterworth filter 2010-02-17 15:54 roboos * benchmark: Created a branches and a tags directory at the highest level of the repository, moved preproc/benchmark from the trunk to branches/benchmarking. In the future there could also be a branches/testing directory. 2010-01-01 21:09 joagro * preproc_hilbert.m: fixed two bugs: 1) angle was computed on non-normalised complex values; 2) unwrapping was performed along wrong dimension; Joachim 2009-12-16 19:38 roboos * preproc_standardize.m: remember the state for updating the mean and variance estimate 2009-12-04 10:00 roboos * COPYING, README, benchmark/benchmark.m, benchmark/benchmark_all.m, benchmark/benchmark_bandpassfilter.m, benchmark/benchmark_bandstopfilter.m, benchmark/benchmark_baselinecorrect.m, benchmark/benchmark_derivative.m, benchmark/benchmark_detrend.m, benchmark/benchmark_dftfilter.m, benchmark/benchmark_highpassfilter.m, benchmark/benchmark_hilbert.m, benchmark/benchmark_lowpassfilter.m, benchmark/benchmark_medianfilter.m, benchmark/benchmark_rectify.m, benchmark/benchmark_rereference.m, benchmark/benchmark_standardize.m, preproc_bandpassfilter.m, preproc_bandstopfilter.m, preproc_baselinecorrect.m, preproc_denoise.m, preproc_derivative.m, preproc_detrend.m, preproc_dftfilter.m, preproc_highpassfilter.m, preproc_hilbert.m, preproc_lowpassfilter.m, preproc_medianfilter.m, preproc_rectify.m, preproc_rereference.m, preproc_standardize.m: set the executable property to OFF on many files that should not be executable (m-files, mex-files, readme, etc.) 2009-11-30 11:28 roboos * preproc_rereference.m: changed all occurences of tabs into 4 spaces 2009-11-30 08:53 roboos * benchmark/benchmark.m, benchmark/benchmark_all.m, benchmark/benchmark_bandpassfilter.m, benchmark/benchmark_bandstopfilter.m, benchmark/benchmark_baselinecorrect.m, benchmark/benchmark_derivative.m, benchmark/benchmark_detrend.m, benchmark/benchmark_dftfilter.m, benchmark/benchmark_highpassfilter.m, benchmark/benchmark_hilbert.m, benchmark/benchmark_lowpassfilter.m, benchmark/benchmark_medianfilter.m, benchmark/benchmark_rectify.m, benchmark/benchmark_rereference.m, benchmark/benchmark_standardize.m, preproc_bandpassfilter.m, preproc_bandstopfilter.m, preproc_baselinecorrect.m, preproc_denoise.m, preproc_derivative.m, preproc_detrend.m, preproc_dftfilter.m, preproc_highpassfilter.m, preproc_hilbert.m, preproc_lowpassfilter.m, preproc_medianfilter.m, preproc_rectify.m, preproc_rereference.m, preproc_standardize.m: changed svn property for keywords Log and Rev 2009-11-30 08:49 roboos * benchmark/benchmark.m, benchmark/benchmark_all.m, benchmark/benchmark_bandpassfilter.m, benchmark/benchmark_bandstopfilter.m, benchmark/benchmark_baselinecorrect.m, benchmark/benchmark_derivative.m, benchmark/benchmark_detrend.m, benchmark/benchmark_dftfilter.m, benchmark/benchmark_highpassfilter.m, benchmark/benchmark_hilbert.m, benchmark/benchmark_lowpassfilter.m, benchmark/benchmark_medianfilter.m, benchmark/benchmark_rectify.m, benchmark/benchmark_rereference.m, benchmark/benchmark_standardize.m, preproc_bandpassfilter.m, preproc_bandstopfilter.m, preproc_baselinecorrect.m, preproc_denoise.m, preproc_derivative.m, preproc_detrend.m, preproc_dftfilter.m, preproc_highpassfilter.m, preproc_hilbert.m, preproc_lowpassfilter.m, preproc_medianfilter.m, preproc_rectify.m, preproc_rereference.m, preproc_standardize.m: changed svn property eol-style to native to ensure consistent end-of-line behaviour on windows and linux 2009-10-27 16:01 roboos * benchmark/benchmark.m, preproc_bandpassfilter.m, preproc_bandstopfilter.m, preproc_baselinecorrect.m, preproc_denoise.m, preproc_derivative.m, preproc_detrend.m, preproc_dftfilter.m, preproc_highpassfilter.m, preproc_hilbert.m, preproc_lowpassfilter.m, preproc_medianfilter.m, preproc_rectify.m, preproc_rereference.m, preproc_standardize.m: removed the old cvs log comments from each of the fieldtrip source code files subversion (a.k.a. svn) does not make use of the special $Log$ keyword, which means that the log messages do not reflect the latest changes you can use 'svn log <filename.m>' or 'svn -v log | less' to get the same detailled information as used to be in the cvs log 2009-10-21 10:25 roboos * ., COPYING, README, benchmark, benchmark/benchmark.m, benchmark/benchmark_all.m, benchmark/benchmark_bandpassfilter.m, benchmark/benchmark_bandstopfilter.m, benchmark/benchmark_baselinecorrect.m, benchmark/benchmark_derivative.m, benchmark/benchmark_detrend.m, benchmark/benchmark_dftfilter.m, benchmark/benchmark_highpassfilter.m, benchmark/benchmark_hilbert.m, benchmark/benchmark_lowpassfilter.m, benchmark/benchmark_medianfilter.m, benchmark/benchmark_rectify.m, benchmark/benchmark_rereference.m, benchmark/benchmark_standardize.m, preproc_bandpassfilter.m, preproc_bandstopfilter.m, preproc_baselinecorrect.m, preproc_denoise.m, preproc_derivative.m, preproc_detrend.m, preproc_dftfilter.m, preproc_highpassfilter.m, preproc_hilbert.m, preproc_lowpassfilter.m, preproc_medianfilter.m, preproc_rectify.m, preproc_rereference.m, preproc_standardize.m: initial import
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Table of Contents
Functions for preprocessing of EEG/MEG data
FieldTrip has a consistent set of low-level functions for reprocessing of EEG and MEG data, such as filtering, baseline correction and re-referencing. This allows other projects to re-use the implemented methods seperate from FieldTrip (e.g. for realtime analysis of EEG and MEG data) and perhaps also to contribute to FieldTrip.
The low-level functions are combined in the preproc toolbox, which is available for download here.
Interface to the preprocessing functions
Note that the FieldTrip toolbox comes with a user-friendly preprocessing function, which reads data from disk and applies preprocessing to that data. Regular users mainly interested in analyzing their data should be using that function. The functions described here are for people that are developing their own code and/or contributing to the development of FieldTrip.
All of the low-level preprocessing functions require data to be represented as a 2D matrix (Nchans X Nsamples). The following functions are implemented
- preproc_bandpassfilter - applies a band-pass filter to the data
- preproc_bandstopfilter - applies a band-stop filter to the data
- preproc_highpassfilter - applies a high-pass filter to the data
- preproc_lowpassfilter - applies a low-pass filter to the data
- preproc_medianfilter - applies a median filter, i.e. a jump-preserving smoothing kernel
- preproc_dftfilter - applies a notch filter to the data to remove the 50Hz noise
- preproc_baselinecorrect - performs a baseline correction
- preproc_detrend - removes linear or higher order polynomial trends
- preproc_derivative - computes the temporal Nth order derivative
- preproc_hilbert - computes the Hilbert transpose of the data
- preproc_rectify - rectifies the data, usefull for EMG
- preproc_rereference - rereferences EEG data using the average over all channels or selected channels
Benchmarking
For real-time use of the functions in this module it is relevant to know how much time each function takes. The execution time depends on the number of channels and on the number of samples in the data block. Assuming that multiple functions are called as part of a larger processing pipeline, the time of the functions that are called has to be summed up.
The benchmarking results presented in the table below were determined with fieldtrip-20090107 and Matlab 7.5 running on a MacPro with 2×2.66 GHz dual-core Intel Xeon processors. Execution time was determined for three representative data block sizes and for various parameters for each function.
The full code for the benchmarking (one script per preproc function and some helper functions) is included in the release version of FieldTrip. You can repeat it on your own workstation and for your own data characteristics.
| function name and algorithm details | 8ch x 100smp | 8ch x 500smp | 64ch x 500smp |
|---|---|---|---|
| preproc_bandpassfilter; Fsample = 1000; Fbp = [ 10 100 ]; order = 2; type = 'but'; dir = 'onepass'; | 1.40 ms | 2.02 ms | 7.10 ms |
| preproc_bandpassfilter; Fsample = 1000; Fbp = [ 10 100 ]; order = 4; type = 'but'; dir = 'onepass'; | 1.68 ms | 2.35 ms | 7.80 ms |
| preproc_bandpassfilter; Fsample = 1000; Fbp = [ 10 100 ]; order = 8; type = 'but'; dir = 'onepass'; | 2.31 ms | 3.04 ms | 8.82 ms |
| preproc_bandpassfilter; Fsample = 1000; Fbp = [ 10 100 ]; order = 16; type = 'fir'; dir = 'onepass'; | 1.20 ms | 1.75 ms | 6.52 ms |
| preproc_bandpassfilter; Fsample = 1000; Fbp = [ 10 100 ]; order = 32; type = 'fir'; dir = 'onepass'; | 1.34 ms | 1.84 ms | 7.05 ms |
| preproc_bandpassfilter; Fsample = 1000; Fbp = [ 10 100 ]; order = 64; type = 'fir'; dir = 'onepass'; | 1.28 ms | 1.97 ms | 7.63 ms |
| function name and algorithm details | 8ch x 100smp | 8ch x 500smp | 64ch x 500smp |
| preproc_bandstopfilter; Fsample = 1000; Fbp = [ 45 55 ]; order = 2; type = 'but'; dir = 'onepass'; | 1.46 ms | 2.11 ms | 7.23 ms |
| preproc_bandstopfilter; Fsample = 1000; Fbp = [ 45 55 ]; order = 4; type = 'but'; dir = 'onepass'; | 1.78 ms | 2.46 ms | 7.97 ms |
| preproc_bandstopfilter; Fsample = 1000; Fbp = [ 45 55 ]; order = 8; type = 'but'; dir = 'onepass'; | 2.59 ms | 3.31 ms | 9.51 ms |
| preproc_bandstopfilter; Fsample = 1000; Fbp = [ 45 55 ]; order = 16; type = 'fir'; dir = 'onepass'; | 1.17 ms | 1.73 ms | 6.47 ms |
| preproc_bandstopfilter; Fsample = 1000; Fbp = [ 45 55 ]; order = 32; type = 'fir'; dir = 'onepass'; | 1.21 ms | 1.79 ms | 6.58 ms |
| preproc_bandstopfilter; Fsample = 1000; Fbp = [ 45 55 ]; order = 64; type = 'fir'; dir = 'onepass'; | 1.26 ms | 1.94 ms | 7.53 ms |
| function name and algorithm details | 8ch x 100smp | 8ch x 500smp | 64ch x 500smp |
| preproc_baselinecorrect; begsample = []; endsample = []; | 0.11 ms | 0.40 ms | 0.93 ms |
| function name and algorithm details | 8ch x 100smp | 8ch x 500smp | 64ch x 500smp |
| preproc_derivative; order = 1; padding = 'end'; | 0.05 ms | 0.18 ms | 0.83 ms |
| preproc_derivative; order = 1; padding = 2; | 0.05 ms | 0.12 ms | 0.51 ms |
| preproc_derivative; order = 1; padding = 3; | 0.05 ms | 0.12 ms | 0.50 ms |
| function name and algorithm details | 8ch x 100smp | 8ch x 500smp | 64ch x 500smp |
| preproc_detrend; begsample = []; endsample = []; order = 1; | 0.12 ms | 0.47 ms | 1.94 ms |
| preproc_detrend; begsample = []; endsample = []; order = 2; | 0.12 ms | 0.56 ms | 2.18 ms |
| preproc_detrend; begsample = []; endsample = []; order = 3; | 0.14 ms | 0.74 ms | 2.43 ms |
| function name and algorithm details | 8ch x 100smp | 8ch x 500smp | 64ch x 500smp |
| preproc_dftfilter; Fsample = 1000; Fline = 50; | 0.13 ms | 0.64 ms | 2.42 ms |
| function name and algorithm details | 8ch x 100smp | 8ch x 500smp | 64ch x 500smp |
| preproc_highpassfilter; Fsample = 1000; Fh = 1; order = 2; type = 'but'; dir = 'onepass'; | 1.28 ms | 1.92 ms | 6.79 ms |
| preproc_highpassfilter; Fsample = 1000; Fh = 1; order = 4; type = 'but'; dir = 'onepass'; | 2.08 ms | 2.23 ms | 7.18 ms |
| preproc_highpassfilter; Fsample = 1000; Fh = 1; order = 8; type = 'but'; dir = 'onepass'; | 2.00 ms | 2.68 ms | 8.00 ms |
| preproc_highpassfilter; Fsample = 1000; Fh = 1; order = 16; type = 'fir'; dir = 'onepass'; | 1.09 ms | 1.67 ms | 6.03 ms |
| preproc_highpassfilter; Fsample = 1000; Fh = 1; order = 32; type = 'fir'; dir = 'onepass'; | 1.12 ms | 1.84 ms | 6.58 ms |
| preproc_highpassfilter; Fsample = 1000; Fh = 1; order = 64; type = 'fir'; dir = 'onepass'; | 1.16 ms | 1.86 ms | 7.56 ms |
| function name and algorithm details | 8ch x 100smp | 8ch x 500smp | 64ch x 500smp |
| preproc_hilbert; option = 'complex'; | 0.26 ms | 1.32 ms | 8.47 ms |
| preproc_hilbert; option = 'abs'; | 0.38 ms | 1.61 ms | 10.42 ms |
| preproc_hilbert; option = 'angle'; | 5.17 ms | 25.37 ms | 44.77 ms |
| function name and algorithm details | 8ch x 100smp | 8ch x 500smp | 64ch x 500smp |
| preproc_lowpassfilter; Fsample = 1000; Fl = 30; order = 2; type = 'but'; dir = 'onepass'; | 1.29 ms | 1.89 ms | 6.91 ms |
| preproc_lowpassfilter; Fsample = 1000; Fl = 30; order = 4; type = 'but'; dir = 'onepass'; | 1.47 ms | 2.17 ms | 7.59 ms |
| preproc_lowpassfilter; Fsample = 1000; Fl = 30; order = 8; type = 'but'; dir = 'onepass'; | 1.92 ms | 2.69 ms | 8.15 ms |
| preproc_lowpassfilter; Fsample = 1000; Fl = 30; order = 16; type = 'fir'; dir = 'onepass'; | 1.16 ms | 1.65 ms | 6.25 ms |
| preproc_lowpassfilter; Fsample = 1000; Fl = 30; order = 32; type = 'fir'; dir = 'onepass'; | 1.09 ms | 1.73 ms | 6.60 ms |
| preproc_lowpassfilter; Fsample = 1000; Fl = 30; order = 64; type = 'fir'; dir = 'onepass'; | 1.15 ms | 1.90 ms | 7.64 ms |
| function name and algorithm details | 8ch x 100smp | 8ch x 500smp | 64ch x 500smp |
| preproc_bandpassfilter; Fsample = 1000; Fbp = [ 10 100 ]; N = 2; type = 'but'; dir = 'onepass'; | 1.40 ms | 2.03 ms | 7.34 ms |
| preproc_bandpassfilter; Fsample = 1000; Fbp = [ 10 100 ]; N = 4; type = 'but'; dir = 'onepass'; | 1.91 ms | 2.42 ms | 7.79 ms |
| preproc_bandpassfilter; Fsample = 1000; Fbp = [ 10 100 ]; N = 8; type = 'but'; dir = 'onepass'; | 2.35 ms | 3.06 ms | 8.87 ms |
| preproc_bandpassfilter; Fsample = 1000; Fbp = [ 10 100 ]; N = 16; type = 'fir'; dir = 'onepass'; | 1.33 ms | 1.75 ms | 6.34 ms |
| preproc_bandpassfilter; Fsample = 1000; Fbp = [ 10 100 ]; N = 32; type = 'fir'; dir = 'onepass'; | 1.32 ms | 1.83 ms | 6.61 ms |
| preproc_bandpassfilter; Fsample = 1000; Fbp = [ 10 100 ]; N = 64; type = 'fir'; dir = 'onepass'; | 1.27 ms | 1.91 ms | 7.47 ms |
| function name and algorithm details | 8ch x 100smp | 8ch x 500smp | 64ch x 500smp |
| preproc_rectify; | 0.03 ms | 0.11 ms | 0.55 ms |
| function name and algorithm details | 8ch x 100smp | 8ch x 500smp | 64ch x 500smp |
| preproc_rereference; refchan = 1; | 0.07 ms | 0.16 ms | 0.55 ms |
| preproc_rereference; refchan = 'all'; | 0.10 ms | 0.25 ms | 1.07 ms |
| function name and algorithm details | 8ch x 100smp | 8ch x 500smp | 64ch x 500smp |
| preproc_standardize; begsample = []; endsample = []; | 0.25 ms | 0.53 ms | 1.73 ms |
Recent changes to the code
