Index of all configuration options

A detailed description of each function is available in the reference documentation.

A

** cfg.absdiff ** - ft_preprocessing
‘no’ or ‘yes’, computes absolute derivative (i.e. first derivative then rectify)

** cfg.absnoise ** - ft_dipolesimulation
add noise with absolute level

** cfg.absnoise ** - ft_connectivitysimulation, ft_connectivitysimulation
scalar (default: 1), specifying the standard deviation of white noise superimposed on top of the simulated signals

** cfg.accuracy_green ** - ft_realtime_headlocalizer
distance from fiducial coordinate; green when within limits (default = 0.15 cm)

** cfg.accuracy_orange ** - ft_realtime_headlocalizer
orange when within limits, red when out (default = 0.3 cm)

** cfg.align ** - ft_spike_waveform
‘yes’ (def). or ‘no’. If ‘yes’, we align all waves to maximum

** cfg.alim ** - ft_rejectvisual
value that determines the amplitude scaling for the channel and trial display, if empty then the amplitude scaling is automatic (default = [])

** cfg.allowoverlap ** - ft_databrowser
‘yes’ or ‘no’, whether data that is overlapping in multiple trials is allowed (default = ‘no’)

** cfg.alpha ** - ft_statistics_analytic, ft_statistics_stats
number, critical value for rejecting the null-hypothesis (default = 0.05)

** cfg.alpha ** - ft_statistics_montecarlo
number, critical value for rejecting the null-hypothesis per tail (default = 0.05)

** cfg.alpha ** - ft_clusterplot
number, highest cluster p-value to be plotted max 0.3 (default = 0.05)

** cfg.alpha ** - ft_sliceinterp
value between 0 and 1 or ‘adaptive’ (default)

** cfg.alphaparam ** - ft_topoplotCC
string, parameter to be used to control the opacity (see below)

** cfg.analyze ** - ft_qualitycheck
string, ‘yes’ or ‘no’ to analyze the dataset (default = ‘yes’)

** cfg.anaparameter ** - ft_sourceplot
string, field in data with the anatomical data (default = ‘anatomy’ if present in data)

** cfg.anonimize ** - ft_audiovideobrowser
[x1 x2 y1 y2], range in pixels for placing a bar over the eyes (default = [])

** cfg.appenddim ** - ft_appendfreq
string, the dimension to concatenate over (default is automatic)

** cfg.appenddim ** - ft_appendtimelock
string, the dimension to concatenate over which to append, this can be ‘chan’ and ‘rpt’ (default is automatic)

** cfg.arrowhead ** - ft_topoplotCC
string, ‘none’, ‘stop’, ‘start’, ‘both’ (default = ‘none’) cfg.arrowsize = scalar, size of the arrow head in figure units, i.e. the same units as the layout (default is automatically determined) cfg.arrowoffset = scalar, amount that the arrow is shifted to the side in figure units, i.e. the same units as the layout (default is automatically determined) cfg.arrowlength = scalar, amount by which the length is reduced relative to the complete line (default = 0.8)

** cfg.artfctdef.clip.amplthreshold ** - ft_artifact_clip
number, minimum amplitude difference in consecutive samples to be considered as ‘clipped’ (default = 0) string, percent of the amplitude range considered as ‘clipped’ (i.e. ‘1%’)

** cfg.artfctdef.clip.channel ** - ft_artifact_clip
Nx1 cell-array with selection of channels, see FT_CHANNELSELECTION for details

** cfg.artfctdef.clip.pretim ** - ft_artifact_clip
0.000; pre-artifact rejection-interval in seconds

** cfg.artfctdef.clip.psttim ** - ft_artifact_clip
0.000; post-artifact rejection-interval in seconds

** cfg.artfctdef.clip.timethreshold ** - ft_artifact_clip
number, minimum duration in seconds of a datasegment with consecutive identical samples to be considered as ‘clipped’

** cfg.artfctdef.crittoilim ** - ft_rejectartifact
when using complete rejection, reject trial only when artifacts occur within this time window (default = whole trial). This only works with in-memory data, since trial time axes are unknown for data on disk.

** cfg.artfctdef.ecg.channel ** - ft_artifact_ecg
Nx1 cell-array with selection of channels, see FT_CHANNELSELECTION for details

** cfg.artfctdef.ecg.cutoff ** - ft_artifact_ecg
3; peak-threshold

** cfg.artfctdef.ecg.inspect ** - ft_artifact_ecg
Nx1 list of channels which will be shown in a QRS-locked average

** cfg.artfctdef.ecg.method ** - ft_artifact_ecg
‘zvalue’; peak-detection method

** cfg.artfctdef.ecg.pretim ** - ft_artifact_ecg
0.05; pre-artifact rejection-interval in seconds

** cfg.artfctdef.ecg.psttim ** - ft_artifact_ecg
0.3; post-artifact rejection-interval in seconds

** cfg.artfctdef.eog.artifact ** - ft_rejectartifact
Nx2 matrix with artifact segments, this is added to the cfg by using FT_ARTIFACT_EOG

** cfg.artfctdef.eog.artpadding ** - ft_artifact_eog
0.1

** cfg.artfctdef.eog.bpfilter ** - ft_artifact_eog
‘yes’

** cfg.artfctdef.eog.bpfiltord ** - ft_artifact_eog
4

** cfg.artfctdef.eog.bpfilttype ** - ft_artifact_eog
‘but’

** cfg.artfctdef.eog.bpfreq ** - ft_artifact_eog
[1 15]

** cfg.artfctdef.eog.channel ** - ft_artifact_eog
Nx1 cell-array with selection of channels, see FT_CHANNELSELECTION for details

** cfg.artfctdef.eog.cutoff ** - ft_artifact_eog
z-value at which to threshold (default = 4)

** cfg.artfctdef.eog.fltpadding ** - ft_artifact_eog
0.1

** cfg.artfctdef.eog.hilbert ** - ft_artifact_eog
‘yes’

** cfg.artfctdef.eog.trlpadding ** - ft_artifact_eog
0.5

** cfg.artfctdef.feedback ** - ft_rejectartifact
‘yes’ or ‘no’ (default = ‘no’)

** cfg.artfctdef.invert ** - ft_rejectartifact
‘yes’ or ‘no’ (default = ‘no’)

** cfg.artfctdef.jump.absdiff ** - ft_artifact_jump
‘yes’

** cfg.artfctdef.jump.artifact ** - ft_rejectartifact
Nx2 matrix with artifact segments, this is added to the cfg by using FT_ARTIFACT_JUMP

** cfg.artfctdef.jump.artpadding ** - ft_artifact_jump
automatically determined based on the filter padding (cfg.padding)

** cfg.artfctdef.jump.channel ** - ft_artifact_jump
Nx1 cell-array with selection of channels, see FT_CHANNELSELECTION for details

** cfg.artfctdef.jump.cutoff ** - ft_artifact_jump
z-value at which to threshold (default = 20)

** cfg.artfctdef.jump.medianfilter ** - ft_artifact_jump
‘yes’

** cfg.artfctdef.jump.medianfiltord ** - ft_artifact_jump
9

** cfg.artfctdef.jump.trlpadding ** - ft_artifact_jump
automatically determined based on the filter padding (cfg.padding)

** cfg.artfctdef.minaccepttim ** - ft_rejectartifact
when using partial rejection, minimum length in seconds of remaining trial (default = 0.1)

** cfg.artfctdef.muscle.artifact ** - ft_rejectartifact
Nx2 matrix with artifact segments, this is added to the cfg by using FT_ARTIFACT_MUSCLE

** cfg.artfctdef.muscle.artpadding ** - ft_artifact_muscle
0.1

** cfg.artfctdef.muscle.boxcar ** - ft_artifact_muscle
0.2

** cfg.artfctdef.muscle.bpfilter ** - ft_artifact_muscle
‘yes’

** cfg.artfctdef.muscle.bpfiltord ** - ft_artifact_muscle
8

** cfg.artfctdef.muscle.bpfilttype ** - ft_artifact_muscle
‘but’

** cfg.artfctdef.muscle.bpfreq ** - ft_artifact_muscle
[110 140]

** cfg.artfctdef.muscle.channel ** - ft_artifact_muscle
Nx1 cell-array with selection of channels, see FT_CHANNELSELECTION for details

** cfg.artfctdef.muscle.cutoff ** - ft_artifact_muscle
z-value at which to threshold (default = 4)

** cfg.artfctdef.muscle.fltpadding ** - ft_artifact_muscle
0.1

** cfg.artfctdef.muscle.hilbert ** - ft_artifact_muscle
‘yes’

** cfg.artfctdef.muscle.trlpadding ** - ft_artifact_muscle
0.1

** cfg.artfctdef.nan.channel ** - ft_artifact_nan
Nx1 cell-array with selection of channels, see FT_CHANNELSELECTION for details

** cfg.artfctdef.reject ** - ft_rejectartifact
‘none’, ‘partial’, ‘complete’, ‘nan’, or ‘value’ (default = ‘complete’)

** cfg.artfctdef.threshold.bpfilter ** - ft_artifact_threshold
‘no’ or ‘yes’ (default = ‘yes’)

** cfg.artfctdef.threshold.bpfiltord ** - ft_artifact_threshold
4

** cfg.artfctdef.threshold.bpfreq ** - ft_artifact_threshold
[0.3 30]

** cfg.artfctdef.threshold.channel ** - ft_artifact_threshold
cell-array with channel labels

** cfg.artfctdef.threshold.max ** - ft_artifact_threshold
value in uV or T, default inf

** cfg.artfctdef.threshold.min ** - ft_artifact_threshold
value in uV or T, default -inf

** cfg.artfctdef.threshold.offset ** - ft_artifact_threshold
value in uV or T, default inf

** cfg.artfctdef.threshold.onset ** - ft_artifact_threshold
value in uV or T, default inf

** cfg.artfctdef.threshold.range ** - ft_artifact_threshold
value in uV or T, default inf

** cfg.artfctdef.tms.channel ** - ft_artifact_tms
Nx1 cell-array with selection of channels, see FT_CHANNELSELECTION for details

** cfg.artfctdef.tms.cutoff ** - ft_artifact_tms
z-value at which to threshold (default = 4)

** cfg.artfctdef.tms.derivative ** - ft_artifact_tms
‘yes’

** cfg.artfctdef.tms.fltpadding ** - ft_artifact_tms
0.1

** cfg.artfctdef.tms.trlpadding ** - ft_artifact_tms
0.1

** cfg.artfctdef.value ** - ft_rejectartifact
scalar value to replace the data in the artifact segments (default = nan)

** cfg.artfctdef.visual.artifact ** - ft_rejectartifact
Nx2 matrix with artifact segments, this is added to the cfg by using FT_DATABROWSER

** cfg.artfctdef.xxx.artifact ** - ft_databrowser
Nx2 matrix with artifact segments see FT_ARTIFACT_xxx functions

** cfg.artfctdef.xxx.artifact ** - ft_rejectartifact
Nx2 matrix with artifact segments, this could be added by your own artifact detection function

** cfg.artfctdef.zvalue.artfctpeak ** - ft_artifact_zvalue
‘yes’ or ‘no’

** cfg.artfctdef.zvalue.artifact ** - ft_rejectartifact
Nx2 matrix with artifact segments, this is added to the cfg by using FT_ARTIFACT_ZVALUE

** cfg.artfctdef.zvalue.artpadding ** - ft_artifact_zvalue

** cfg.artfctdef.zvalue.baselinewindow ** - ft_artifact_zvalue
[begin end] in seconds, the default is the complete trial

** cfg.artfctdef.zvalue.bpfilter ** - ft_artifact_zvalue
‘no’ or ‘yes’ bandpass filter

** cfg.artfctdef.zvalue.bpfiltord ** - ft_artifact_zvalue
bandpass filter order

** cfg.artfctdef.zvalue.bpfilttype ** - ft_artifact_zvalue
digital filter type, ‘but’ (default) or ‘firws’ or ‘fir’ or ‘firls’

** cfg.artfctdef.zvalue.bpfreq ** - ft_artifact_zvalue
bandpass frequency range, specified as [low high] in Hz

** cfg.artfctdef.zvalue.bsfilter ** - ft_artifact_zvalue
‘no’ or ‘yes’ bandstop filter for line noise removal

** cfg.artfctdef.zvalue.bsfiltord ** - ft_artifact_zvalue
bandstop filter order

** cfg.artfctdef.zvalue.bsfilttype ** - ft_artifact_zvalue
digital filter type, ‘but’ (default) or ‘firws’ or ‘fir’ or ‘firls’

** cfg.artfctdef.zvalue.bsfreq ** - ft_artifact_zvalue
bandstop frequency range, specified as [low high] in Hz

** cfg.artfctdef.zvalue.channel ** - ft_artifact_zvalue

** cfg.artfctdef.zvalue.cutoff ** - ft_artifact_zvalue

** cfg.artfctdef.zvalue.demean ** - ft_artifact_zvalue
‘no’ or ‘yes’

** cfg.artfctdef.zvalue.detrend ** - ft_artifact_zvalue
‘no’ or ‘yes’

** cfg.artfctdef.zvalue.dftfilter ** - ft_artifact_zvalue
‘no’ or ‘yes’ line noise removal using discrete fourier transform

** cfg.artfctdef.zvalue.fltpadding ** - ft_artifact_zvalue

** cfg.artfctdef.zvalue.hilbert ** - ft_artifact_zvalue
‘no’ or ‘yes’

** cfg.artfctdef.zvalue.hpfilter ** - ft_artifact_zvalue
‘no’ or ‘yes’ highpass filter

** cfg.artfctdef.zvalue.hpfiltord ** - ft_artifact_zvalue
highpass filter order

** cfg.artfctdef.zvalue.hpfilttype ** - ft_artifact_zvalue
digital filter type, ‘but’ (default) or ‘firws’ or ‘fir’ or ‘firls’

** cfg.artfctdef.zvalue.hpfreq ** - ft_artifact_zvalue
highpass frequency in Hz

** cfg.artfctdef.zvalue.interactive ** - ft_artifact_zvalue
‘yes’ or ‘no’

** cfg.artfctdef.zvalue.lpfilter ** - ft_artifact_zvalue
‘no’ or ‘yes’ lowpass filter

** cfg.artfctdef.zvalue.lpfiltord ** - ft_artifact_zvalue
lowpass filter order

** cfg.artfctdef.zvalue.lpfilttype ** - ft_artifact_zvalue
digital filter type, ‘but’ (default) or ‘firws’ or ‘fir’ or ‘firls’

** cfg.artfctdef.zvalue.lpfreq ** - ft_artifact_zvalue
lowpass frequency in Hz

** cfg.artfctdef.zvalue.medianfilter ** - ft_artifact_zvalue
‘no’ or ‘yes’ jump preserving median filter

** cfg.artfctdef.zvalue.medianfiltord ** - ft_artifact_zvalue
length of median filter

** cfg.artfctdef.zvalue.rectify ** - ft_artifact_zvalue
‘no’ or ‘yes’

** cfg.artfctdef.zvalue.trlpadding ** - ft_artifact_zvalue

** cfg.artifact ** - ft_removetemplateartifact
Mx2 matrix with sample numbers of the artifact segments, e.g. obtained from FT_ARTIFACT_EOG

** cfg.asymmetry ** - ft_freqsimulation
amount of asymmetry (default = 0, which is none)

** cfg.atlas ** - ft_sourceplot
string, filename of atlas to use (default = []) see FT_READ_ATLAS for ROI masking (see ‘masking’ below) or for orthogonal plots (see method=’ortho’ below)

** cfg.atlas ** - ft_volumelookup, ft_volumelookup, ft_volumelookup
string, filename of atlas to use, see FT_READ_ATLAS

** cfg.audiofile ** - ft_audiovideobrowser
string with the filename

** cfg.audiohdr ** - ft_audiovideobrowser
header structure of the audio data, see FT_READ_HEADER

** cfg.avgoverchan ** - ft_spiketriggeredspectrum_stat
‘weighted’, ‘unweighted’ (default) or ‘no’. This regulates averaging of fourierspectra prior to computing the statistic. - ‘weighted’ : we average across channels by weighting by the LFP power. This is identical to adding the raw LFP signals in time and then taking their FFT. - ‘unweighted’: we average across channels after normalizing for LFP power. This is identical to normalizing LFP signals for their power, averaging them, and then taking their FFT. - ‘no’ : no weighting is performed, statistic is computed for every LFP channel.

** cfg.avgoverchan ** - ft_freqstatistics, ft_timelockstatistics
‘yes’ or ‘no’ (default = ‘no’)

** cfg.avgoverfreq ** - ft_freqstatistics
‘yes’ or ‘no’ (default = ‘no’)

** cfg.avgoverfreq ** - ft_sourceplot
string, can be ‘yes’ or ‘no’ (default = ‘no’)

** cfg.avgovertime ** - ft_freqstatistics, ft_timelockstatistics
‘yes’ or ‘no’ (default = ‘no’)

** cfg.avgovertime ** - ft_sourceplot
string, can be ‘yes’ or ‘no’ (default = ‘no’)

** cfg.axes ** - ft_multiplotER
string, ‘yes’ or ‘no’ whether to draw x- and y-axes for each graph (default = ‘yes’)

** cfg.axis ** - ft_sourceplot
‘on’ or ‘off’ (default = ‘on’)

** cfg.axisfontsize ** - ft_databrowser
number, fontsize along the axes (default = 10)

** cfg.axisfontunits ** - ft_databrowser
string, can be ‘normalized’, ‘points’, ‘pixels’, ‘inches’ or ‘centimeters’ (default = ‘points’)

B

** cfg.backproject ** - ft_prepare_leadfield
‘yes’ or ‘no’ (default = ‘yes’) determines when reducerank is applied whether the lower rank leadfield is projected back onto the original linear subspace, or not.

** cfg.badchannel ** - ft_channelrepair
cell-array, see FT_CHANNELSELECTION for details

** cfg.bandwidth ** - ft_connectivityanalysis
scalar, (default = Rayleigh frequency), needed for

** cfg.baseline ** - ft_multiplotTFR, ft_singleplotTFR
‘yes’, ‘no’ or [time1 time2] (default = ‘no’), see FT_FREQBASELINE

** cfg.baseline ** - ft_multiplotER
‘yes’, ‘no’ or [time1 time2] (default = ‘no’), see FT_TIMELOCKBASELINE or FT_FREQBASELINE

** cfg.baseline ** - ft_singleplotER
‘yes’, ‘no’ or [time1 time2] (default = ‘no’), see ft_timelockbaseline

** cfg.baseline ** - ft_movieplotER, ft_movieplotTFR, ft_topoplotER, ft_topoplotTFR
‘yes’,’no’ or [time1 time2] (default = ‘no’), see FT_TIMELOCKBASELINE or FT_FREQBASELINE

** cfg.baseline ** - ft_prepare_headmodel
(optional)

** cfg.baseline ** - ft_timelockbaseline
[begin end] (default = ‘no’)

** cfg.baseline ** - ft_freqbaseline
[begin end] (default = ‘no’), alternatively an Nfreq x 2 matrix can be specified, that provides frequency specific baseline windows.

** cfg.baseline ** - ft_timelocksimulation
number (default = 0.3)

** cfg.baseline ** - ft_steadystatesimulation
scalar, baseline length in seconds (default = 0)

** cfg.baselinetype ** - ft_movieplotER, ft_movieplotTFR, ft_singleplotER, ft_topoplotER, ft_topoplotTFR
‘absolute’ or ‘relative’ (default = ‘absolute’)

** cfg.baselinetype ** - ft_multiplotTFR, ft_singleplotTFR
‘absolute’, ‘relative’, ‘relchange’ or ‘db’ (default = ‘absolute’)

** cfg.baselinetype ** - ft_freqbaseline
‘absolute’, ‘relative’, ‘relchange’, ‘normchange’ or ‘db’ (default = ‘absolute’)

** cfg.baselinewindow ** - ft_combineplanar
[begin end]

** cfg.baselinewindow ** - ft_connectivitysimulation, ft_connectivitysimulation
[begin end] in seconds, the default is the complete trial

** cfg.baselinewindow ** - ft_preprocessing, ft_resampledata
[begin end] in seconds, the default is the complete trial (default = ‘all’)

** cfg.baudrate ** - ft_omri_quality
serial port baudrate (default = 19200)

** cfg.begsample ** - ft_redefinetrial
single number or Nx1 vector, expressed in samples relative to the start of the input trial

** cfg.binica.annealdeg ** - ft_componentanalysis

** cfg.binica.annealstep ** - ft_componentanalysis

** cfg.binica.bias ** - ft_componentanalysis

** cfg.binica.blocksize ** - ft_componentanalysis

** cfg.binica.extended ** - ft_componentanalysis

** cfg.binica.filenum ** - ft_componentanalysis

** cfg.binica.lrate ** - ft_componentanalysis

** cfg.binica.maxsteps ** - ft_componentanalysis

** cfg.binica.momentum ** - ft_componentanalysis

** cfg.binica.pca ** - ft_componentanalysis

** cfg.binica.posact ** - ft_componentanalysis

** cfg.binica.sphering ** - ft_componentanalysis

** cfg.binica.stop ** - ft_componentanalysis

** cfg.binica.verbose ** - ft_componentanalysis

** cfg.binica.weightsin ** - ft_componentanalysis

** cfg.bins ** - ft_spike_isi
ascending vector of isi bin edges.

** cfg.binsize ** - ft_spike_xcorr
[binsize] in sec (default = 0.001 sec).

** cfg.binsize ** - ft_spike_psth
[binsize] in sec or string. If ‘scott’, we estimate the optimal bin width using Scott’s formula (1979). If ‘sqrt’, we take the number of bins as the square root of the number of observations. The optimal bin width is derived over all neurons; thus, this procedure works best if the input contains only one neuron at a time.

** cfg.blocksize ** - ft_databrowser
duration in seconds for cutting the data up

** cfg.blocksize ** - ft_realtime_coillocalizer, ft_realtime_headlocalizer, ft_realtime_ouunpod
number, size of the blocks/chuncks that are processed (default = 1 second)

** cfg.bootstrap ** - ft_sourceanalysis
‘no’ or ‘yes’ bootstrap resampling of trials

** cfg.borderspikes ** - ft_spiketriggeredspectrum_convol
‘no’, or if cfg.rejectsaturation = ‘yes’, or if the trial length was too short for the window desired.

** cfg.box ** - ft_multiplotTFR
‘yes’, ‘no’ (default = ‘no’ if maskparameter given default = ‘yes’) Draw a box around each graph

** cfg.box ** - ft_volumelookup
Nx3 vector, size of each box in cm/mm dep on unit of input

** cfg.box ** - ft_layoutplot
string, ‘yes’ or ‘no’ whether box should be plotted around electrode (default = ‘yes’)

** cfg.box ** - ft_multiplotER
string, ‘yes’ or ‘no’ whether to draw a box around each graph (default = ‘no’)

** cfg.boxchannel ** - ft_prepare_layout
‘all’, or Nx1 cell-array with selection of channels, see FT_CHANNELSELECTION for details specificies channels to use for determining channel box size (default = ‘all’, recommended for MEG/EEG, a selection is recommended for iEEG)

** cfg.bpfiltdev ** - ft_preprocessing
bandpass max passband deviation (firws with ‘kaiser’ window, default 0.001 set in low-level function)

** cfg.bpfiltdf ** - ft_preprocessing
bandpass transition width (firws, overrides order, default set in low-level function)

** cfg.bpfiltdir ** - ft_preprocessing
filter direction, ‘twopass’ (default), ‘onepass’ or ‘onepass-reverse’ or ‘onepass-zerophase’ (default for firws) or ‘onepass-minphase’ (firws, non-linear!)

** cfg.bpfilter ** - ft_preprocessing
‘no’ or ‘yes’ bandpass filter (default = ‘no’)

** cfg.bpfilter ** - ft_connectivitysimulation, ft_connectivitysimulation
‘yes’ (or ‘no’)

** cfg.bpfiltord ** - ft_preprocessing
bandpass filter order (default set in low-level function)

** cfg.bpfilttype ** - ft_preprocessing
digital filter type, ‘but’ or ‘firws’ or ‘fir’ or ‘firls’ (default = ‘but’)

** cfg.bpfiltwintype ** - ft_preprocessing
bandpass window type, ‘hann’ or ‘hamming’ (default) or ‘blackman’ or ‘kaiser’ (firws)

** cfg.bpfreq ** - ft_connectivitysimulation, ft_connectivitysimulation
[bplow bphigh] (default: [15 25])

** cfg.bpfreq ** - ft_preprocessing
bandpass frequency range, specified as [lowFreq highFreq] in Hz

** cfg.bpfreq ** - ft_connectivitysimulation
nxnx2 matrix, specifying the lower and upper frequencies of the bands that are transmitted, rows causing column

** cfg.bpinstabilityfix ** - ft_preprocessing
deal with filter instability, ‘no’, ‘reduce’, ‘split’ (default = ‘no’)

** cfg.brainsmooth ** - ft_volumesegment
‘no’, or scalar, the FWHM of the gaussian kernel in voxels, (default = 5)

** cfg.brainthreshold ** - ft_volumesegment
‘no’, or scalar, relative threshold value which is used to threshold the tpm in order to create a volumetric brainmask (see below), (default = 0.5)

** cfg.bsfiltdev ** - ft_preprocessing
bandstop max passband deviation (firws with ‘kaiser’ window, default 0.001 set in low-level function)

** cfg.bsfiltdf ** - ft_preprocessing
bandstop transition width (firws, overrides order, default set in low-level function)

** cfg.bsfiltdir ** - ft_preprocessing
filter direction, ‘twopass’ (default), ‘onepass’ or ‘onepass-reverse’ or ‘onepass-zerophase’ (default for firws) or ‘onepass-minphase’ (firws, non-linear!)

** cfg.bsfilter ** - ft_preprocessing
‘no’ or ‘yes’ bandstop filter (default = ‘no’)

** cfg.bsfiltord ** - ft_preprocessing
bandstop filter order (default set in low-level function)

** cfg.bsfilttype ** - ft_preprocessing
digital filter type, ‘but’ or ‘firws’ or ‘fir’ or ‘firls’ (default = ‘but’)

** cfg.bsfiltwintype ** - ft_preprocessing
bandstop window type, ‘hann’ or ‘hamming’ (default) or ‘blackman’ or ‘kaiser’ (firws)

** cfg.bsfreq ** - ft_preprocessing
bandstop frequency range, specified as [low high] in Hz (or as Nx2 matrix for notch filter)

** cfg.bsinstabilityfix ** - ft_preprocessing
deal with filter instability, ‘no’, ‘reduce’, ‘split’ (default = ‘no’)

** cfg.bufferdata ** - ft_realtime_coillocalizer
causes the realtime function to jump to the last

** cfg.bufferdata ** - ft_realtime_coillocalizer
whether to process the ‘first or ‘last’ data that is available (default = ‘last’)

** cfg.bufferdata ** - ft_realtime_headlocalizer, ft_realtime_ouunpod
whether to start on the ‘first or ‘last’ data that is available (default = ‘last’)

** cfg.bw ** - ft_prepare_layout
‘yes’ or ‘no’, if an image is used and this option is true, the image is transformed in black and white (default = ‘no’, i.e. do not transform)

C

** cfg.calibration ** - ft_spikedownsample
optional scaling factor to apply to the data to convert it in uV, see below

** cfg.camlight ** - ft_sourceplot
‘yes’ or ‘no’ (default = ‘yes’)

** cfg.casesensitive ** - ft_electroderealign
‘yes’ or ‘no’, determines whether string comparisons between electrode labels are case sensitive (default = ‘yes’)

** cfg.channel ** - ft_mvaranalysis
‘all’ (default) or list of channels for which an mvar model is fitted. (Do NOT specify if cfg.channelcmb is defined)

** cfg.channel ** - ft_stratify
‘all’ or list with indices ( default = ‘all’)

** cfg.channel ** - ft_prepare_layout
‘all’, or Nx1 cell-array with selection of channels, see FT_CHANNELSELECTION for details

** cfg.channel ** - ft_channelnormalise
‘all’, or a selection of channels

** cfg.channel ** - ft_connectivityanalysis
Nx1 cell-array containing a list of channels which are used for the subsequent computations. This only has an effect when the input data is univariate. See FT_CHANNELSELECTION

** cfg.channel ** - ft_spiketriggeredspectrum_stat
Nx1 cell-array or numerical array with selection of channels (default = ‘all’),See CHANNELSELECTION for details

** cfg.channel ** - ft_megplanar
Nx1 cell-array with selection of channels (default = ‘MEG’), see FT_CHANNELSELECTION for details

** cfg.channel ** - ft_nonlinearassociation
Nx1 cell-array with selection of channels (default = ‘all’), see CHANNELSELECTION for details

** cfg.channel ** - ft_denoise_dssp, ft_dipolefitting, ft_dipolesimulation, ft_electroderealign, ft_freqanalysis, ft_freqdescriptives, ft_freqgrandaverage, ft_freqstatistics, ft_globalmeanfield, ft_multiplotER, ft_multiplotTFR, ft_prepare_leadfield, ft_preprocessing, ft_rejectvisual, ft_removetemplateartifact, ft_singleplotTFR, ft_sourceanalysis, ft_spikedownsample, ft_spikesplitting, ft_spiketriggeredaverage, ft_spiketriggeredinterpolation, ft_timelockanalysis, ft_timelockgrandaverage, ft_timelockstatistics, ft_topoplotER, ft_topoplotTFR
Nx1 cell-array with selection of channels (default = ‘all’), see FT_CHANNELSELECTION for details

** cfg.channel ** - ft_electrodeplacement
Nx1 cell-array with selection of channels (default = {‘1’ ‘2’ …})

** cfg.channel ** - ft_detect_movement
Nx1 cell-array with selection of channels, see FT_CHANNELSELECTION for details, (default = ‘all’)

** cfg.channel ** - ft_databrowser
cell-array with channel labels, see FT_CHANNELSELECTION

** cfg.channel ** - ft_componentanalysis, ft_spikesorting
cell-array with channel selection (default = ‘all’), see FT_CHANNELSELECTION for details

** cfg.channel ** - ft_crossfrequencyanalysis
cell-array with selection of channels, see FT_CHANNELSELECTION

** cfg.channel ** - ft_timelockbaseline
cell-array, see FT_CHANNELSELECTION

** cfg.channel ** - ft_realtime_oddball, ft_realtime_ouunpod
cell-array, see FT_CHANNELSELECTION (default = ‘all’)

** cfg.channel ** - ft_realtime_coillocalizer
cell-array, see FT_CHANNELSELECTION (default = {‘MEG’, ‘MEGREF’})

** cfg.channel ** - ft_prepare_neighbours
channels for which neighbours should be found

** cfg.channel ** - ft_connectivityplot
list of channels to be included for the plotting (default = ‘all’), see FT_CHANNELSELECTION for details

** cfg.channel ** - ft_singleplotER
nx1 cell-array with selection of channels (default = ‘all’) see ft_channelselection for details

** cfg.channel ** - ft_electrodermalactivity, ft_heartrate, ft_respiration
selected channel for processing, see FT_CHANNELSELECTION

** cfg.channel ** - ft_denoise_pca
the channels to be denoised (default = ‘MEG’)

** cfg.channelclamped ** - ft_databrowser
cell-array with channel labels, that (when using the ‘vertical’ viewmode) will always be shown at the bottom. This is useful for showing ECG/EOG channels along with the other channels

** cfg.channelcmb ** - ft_freqanalysis, ft_spike_jpsth, ft_spike_xcorr
Mx2 cell-array with selection of channel pairs (default = {‘all’ ‘all’}), see FT_CHANNELCOMBINATION for details

** cfg.channelcmb ** - ft_lateralizedpotential
Nx2 cell array

** cfg.channelcmb ** - ft_connectivityanalysis
Nx2 cell-array containing the channel combinations on which to compute the connectivity. This only has an effect when the input data is univariate. See FT_CHANNELCOMBINATION

** cfg.channelcmb ** - ft_mvaranalysis
specify channel combinations as a two-column cell array with channels in each column between which a bivariate model will be fit (overrides cfg.channel)

** cfg.channelcmb ** - ft_spike_plot_jpsth
string or index of single channel combination to trigger on. See SPIKESTATION_FT_SUB_CHANNELCOMBINATION for details.

** cfg.channelcmb ** - ft_lateralizedpotential
{‘Fp1’ ‘Fp2’ ‘F7’ ‘F8’ ‘F3’ ‘F4’ ‘T7’ ‘T8’ ‘C3’ ‘C4’ ‘P7’ ‘P8’ ‘P3’ ‘P4’ ‘O1’ ‘O2’}

** cfg.channelcolormap ** - ft_databrowser
COLORMAP (default = customized lines map with 15 colors)

** cfg.channelprefix ** - ft_spikedownsample
string, will be added to channel name, e.g. ‘lfp’ -> ‘lfp_ncs001’ (default = [])

** cfg.chanscale ** - ft_databrowser
Nx1 vector with scaling factors, one per channel specified in cfg.channel

** cfg.chantype ** - ft_preprocessing
string or Nx1 cell-array with channel types to be read (only for NeuroOmega)

** cfg.chanunit ** - ft_dipolesimulation
units for the channel data

** cfg.clim ** - ft_volumerealign
[min max], scaling of the anatomy color (default is to adjust to the minimum and maximum)

** cfg.clim ** - ft_electrodeplacement
color range of the data (default = [0 1], i.e. the full range)

** cfg.clim ** - ft_sourceplot
lower and upper anatomical MRI limits (default = [0 1])

** cfg.clipVar ** - ft_omri_quality
threshold to clip variation plot with as a fraction of signal magnitude (default=0.2)

** cfg.clipmax ** - ft_sliceinterp
value or ‘auto’ (clipping of source data)

** cfg.clipmin ** - ft_sliceinterp
value or ‘auto’ (clipping of source data)

** cfg.clipsym ** - ft_sliceinterp
‘yes’ or ‘no’ (default) symmetrical clipping

** cfg.cloudtype ** - ft_sourceplot
‘point’ plots a single point at each sensor position ‘cloud’ (default) plots each a group of spherically arranged points at each sensor position ‘surf’ plots a single spherical surface mesh at each sensor position

** cfg.clusteralpha ** - ft_statistics_montecarlo
for either parametric or nonparametric thresholding per tail (default = 0.05)

** cfg.clustercritval ** - ft_statistics_montecarlo
for parametric thresholding (default is determined by the statfun)

** cfg.clusterstatistic ** - ft_statistics_montecarlo
how to combine the single samples that belong to a cluster, ‘maxsum’, ‘maxsize’, ‘wcm’ (default = ‘maxsum’) option ‘wcm’ refers to ‘weighted cluster mass’, a statistic that combines cluster size and intensity; see Hayasaka & Nichols (2004) NeuroImage for details

** cfg.clustertail ** - ft_statistics_montecarlo
-1, 1 or 0 (default = 0)

** cfg.clusterthreshold ** - ft_statistics_montecarlo
method for single-sample threshold, ‘parametric’, ‘nonparametric_individual’, ‘nonparametric_common’ (default = ‘parametric’)

** cfg.cmapneurons ** - ft_spike_plot_raster
‘auto’ (default), or nUnits-by-3 matrix. Controls coloring of spikes and psth/density data if multiple cells are present.

** cfg.cohmethod ** - ft_sourcedescriptives
‘regular’, ‘lambda1’, ‘canonical’

** cfg.coilaccuracy ** - ft_preprocessing
can be empty or a number (0, 1 or 2) to specify the accuracy (default = [])

** cfg.coilfreq ** - ft_realtime_coillocalizer
single number in Hz or list of numbers

** cfg.coilfreq ** - ft_realtime_headlocalizer
single number in Hz or list of numbers (default = [293, 307, 314, 321, 328])

** cfg.colmax ** - ft_sliceinterp
source value mapped to the highest color (default = ‘auto’)

** cfg.colmin ** - ft_sliceinterp
source value mapped to the lowest color (default = ‘auto’)

** cfg.colorbar ** - ft_topoplotER, ft_topoplotIC, ft_topoplotTFR
‘yes’ ‘no’ (default) ‘North’ inside plot box near top ‘South’ inside bottom ‘East’ inside right ‘West’ inside left ‘NorthOutside’ outside plot box near top ‘SouthOutside’ outside bottom ‘EastOutside’ outside right ‘WestOutside’ outside left

** cfg.colorbar ** - ft_spike_plot_jpsth
‘yes’ (default) or ‘no’

** cfg.colorbar ** - ft_sourceplot
‘yes’ or ‘no’ (default = ‘yes’)

** cfg.colorbar ** - ft_movieplotER, ft_movieplotTFR, ft_multiplotTFR
‘yes’, ‘no’ (default = ‘no’)

** cfg.colorbar ** - ft_singleplotTFR
‘yes’, ‘no’ (default = ‘yes’)

** cfg.colorgrad ** - ft_sourceplot
‘white’ or a scalar (e.g. 1), degree to which color of points in cloud changes from its center

** cfg.colorgroups ** - ft_databrowser
‘sequential’ ‘allblack’ ‘labelcharx’ (x = xth character in label), ‘chantype’ or vector with length(data/hdr.label) defining groups (default = ‘sequential’)

** cfg.colormap ** - ft_spike_plot_isireturn
N-by-3 colormap (see COLORMAP). Default = hot(256);

** cfg.colormap ** - ft_spike_plot_jpsth
N-by-3 colormap (see COLORMAP). or ‘auto’ (default,hot(256))

** cfg.colormap ** - ft_multiplotTFR, ft_singleplotTFR, ft_topoplotER, ft_topoplotIC, ft_topoplotTFR
any sized colormap, see COLORMAP

** cfg.colormap ** - ft_sliceinterp
colormap for source overlay (default is jet(128))

** cfg.colorparam ** - ft_topoplotCC
string, parameter to be used to control the line color

** cfg.comment ** - ft_topoplotER
‘no’, ‘auto’ or ‘xlim’ (default = ‘auto’) ‘auto’: date, xparam and zparam limits are printed ‘xlim’: only xparam limits are printed

** cfg.comment ** - ft_topoplotTFR
‘no’, ‘auto’ or ‘xlim’ (default = ‘auto’) ‘auto’: date, xparam, yparam and parameter limits are printed ‘xlim’: only xparam limits are printed ‘ylim’: only yparam limits are printed

** cfg.comment ** - ft_annotate
string

** cfg.comment ** - ft_topoplotIC
string ‘no’ ‘auto’ or ‘xlim’ (default = ‘auto’) ‘auto’: date, xparam and zparam limits are printed ‘xlim’: only xparam limits are printed

** cfg.comment ** - ft_multiplotER, ft_multiplotTFR
string of text (default = date + limits) Add ‘comment’ to graph (according to COMNT in the layout)

** cfg.commentpos ** - ft_topoplotER, ft_topoplotIC, ft_topoplotTFR
string or two numbers, position of comment (default ‘leftbottom’) ‘lefttop’ ‘leftbottom’ ‘middletop’ ‘middlebottom’ ‘righttop’ ‘rightbottom’ ‘title’ to place comment as title ‘layout’ to place comment as specified for COMNT in layout [x y] coordinates

** cfg.complex ** - ft_connectivityanalysis
‘abs’ (default), ‘angle’, ‘complex’, ‘imag’, ‘real’, ‘-logabs’, support for method ‘coh’, ‘csd’, ‘plv’

** cfg.component ** - ft_dipolefitting
array with numbers (can be empty -> all)

** cfg.component ** - ft_topoplotIC
field that contains the independent component(s) to be plotted as color

** cfg.component ** - ft_rejectcomponent
list of components to remove, e.g. [1 4 7] or see FT_CHANNELSELECTION

** cfg.compscale ** - ft_databrowser
string, ‘global’ or ‘local’, defines whether the colormap for the topographic scaling is applied per topography or on all visualized components (default ‘global’)

** cfg.conductivity ** - ft_prepare_headmodel, ft_prepare_headmodel

** cfg.conductivity ** - ft_prepare_headmodel
a number or a vector containing the conductivities of the compartments

** cfg.conductivity ** - ft_scalpcurrentdensity, ft_scalpcurrentdensity
conductivity of the skin (default = 0.33 S/m)

** cfg.confound ** - ft_regressconfound
matrix, [Ntrials X Nconfounds], may not contain NaNs

** cfg.continuous ** - ft_artifact_clip, ft_artifact_ecg, ft_artifact_eog, ft_artifact_jump, ft_artifact_muscle, ft_artifact_threshold
‘yes’ or ‘no’ whether the file contains continuous data

** cfg.continuous ** - ft_artifact_tms, ft_artifact_zvalue
‘yes’ or ‘no’ whether the file contains continuous data (default = ‘yes’)

** cfg.continuous ** - ft_preprocessing
‘yes’ or ‘no’ whether the file contains continuous data (default is determined automatic)

** cfg.continuous ** - ft_databrowser
‘yes’ or ‘no’, whether the data should be interpreted as continuous or trial-based

** cfg.coordsys ** - ft_volumerealign
string specifying the origin and the axes of the coordinate system. Supported coordinate systems are ‘ctf’, ‘4d’, ‘bti’, ‘yokogawa’, ‘asa’, ‘itab’, ‘neuromag’, ‘acpc’, and ‘paxinos’. See http://tinyurl.com/ojkuhqz

** cfg.coordsys ** - ft_preprocessing
string, ‘head’ or ‘dewar’ (default = ‘head’)

** cfg.coordsys ** - ft_meshrealign
string, can be ‘ctf’, ‘neuromag’, ‘4d’, ‘bti’, ‘itab’

** cfg.correctMotion ** - ft_omri_pipeline, ft_omri_pipeline_nuisance
= flag indicating whether to correct motion artifacts (default = 1 = yes)

** cfg.correctSliceTime ** - ft_omri_pipeline, ft_omri_pipeline_nuisance
flag indicating whether to correct slice timing (default = 1 = yes)

** cfg.correctm ** - ft_statistics_analytic
string, apply multiple-comparison correction, ‘no’, ‘bonferroni’, ‘holm’, ‘hochberg’, ‘fdr’ (default = ‘no’)

** cfg.correctm ** - ft_statistics_montecarlo
string, apply multiple-comparison correction, ‘no’, ‘max’, cluster’, ‘bonferroni’, ‘holm’, ‘hochberg’, ‘fdr’ (default = ‘no’)

** cfg.correcttail ** - ft_statistics_montecarlo
string, correct p-values or alpha-values when doing a two-sided test, ‘alpha’,’prob’ or ‘no’ (default = ‘no’)

** cfg.coupling ** - ft_connectivitysimulation
nxn matrix, specifying coupling strength, rows causing column

** cfg.covariance ** - ft_timelockanalysis
‘no’ or ‘yes’ (default = ‘no’)

** cfg.covariancewindow ** - ft_timelockanalysis
[begin end] in seconds, or ‘all’, ‘minperiod’, ‘maxperiod’, ‘prestim’, ‘poststim’ (default = ‘all’)

** cfg.covmat ** - ft_connectivitysimulation
covariance matrix between the signals

** cfg.crosshair ** - ft_sourceplot
‘yes’ or ‘no’ (default = ‘yes’)

** cfg.csp.classlabels ** - ft_componentanalysis
vector that assigns a trial to class 1 or 2.

** cfg.csp.numfilters ** - ft_componentanalysis
the number of spatial filters to use (default: 6).

** cfg.cvar ** - ft_statistics_montecarlo
number or list with indices, control variable(s)

D

** cfg.datafile ** - ft_realtime_coillocalizer, ft_realtime_oddball, ft_realtime_ouunpod
string

** cfg.datafile ** - ft_artifact_clip, ft_artifact_ecg, ft_artifact_eog, ft_artifact_jump, ft_artifact_muscle, ft_artifact_threshold, ft_artifact_tms, ft_artifact_zvalue, ft_databrowser, ft_preprocessing
string with the filename

** cfg.dataformat ** - ft_artifact_ecg, ft_artifact_eog, ft_artifact_jump, ft_artifact_muscle, ft_artifact_threshold, ft_artifact_tms, ft_artifact_zvalue

** cfg.dataformat ** - ft_spikedetection
string with the output dataset format, see FT_WRITE_FCDC_SPIKE

** cfg.dataformat ** - ft_spikedownsample
string with the output dataset format, see WRITE_DATA

** cfg.dataformat ** - ft_realtime_coillocalizer, ft_realtime_oddball, ft_realtime_ouunpod
string, default is determined automatic

** cfg.datahdr ** - ft_audiovideobrowser
header structure of the EEG/MEG data, see FT_READ_HEADER

** cfg.dataset ** - ft_qualitycheck
a string (e.g. ‘dataset.ds’)

** cfg.dataset ** - ft_definetrial
pathname to dataset from which to read the events

** cfg.dataset ** - ft_realtime_coillocalizer, ft_realtime_oddball, ft_realtime_ouunpod
string

** cfg.dataset ** - ft_artifact_clip, ft_artifact_ecg, ft_artifact_eog, ft_artifact_jump, ft_artifact_muscle, ft_artifact_threshold, ft_artifact_tms, ft_artifact_zvalue, ft_databrowser, ft_headmovement, ft_preprocessing
string with the filename

** cfg.dataset ** - ft_spikedetection, ft_spikedownsample
string with the input dataset

** cfg.dataset ** - ft_spikefixdmafile, ft_spikesplitting
string with the name of the DMA log file

** cfg.dataset ** - ft_realtime_headlocalizer
string, name or location of a dataset/buffer (default = ‘buffer://odin:1972’)

** cfg.datatype ** - ft_volumewrite
‘bit1’, ‘uint8’, ‘int16’, ‘int32’, ‘float’ or ‘double’

** cfg.degree ** - ft_scalpcurrentdensity
degree of legendre polynomials (default for <=32 electrodes = 9, <=64 electrodes = 14, <=128 electrodes = 20, else = 32

** cfg.delay ** - ft_connectivitysimulation
delay vector between the signals in samples

** cfg.delay ** - ft_connectivitysimulation
matrix, [nsignal x number of unobserved signals] specifying the time shift (in samples) between the unobserved signals and the observed signals

** cfg.delay ** - ft_connectivitysimulation
nxn matrix, specifying the delay, in seconds, from one signal’s spectral component to the other signal, rows causing column

** cfg.delaystep ** - ft_nonlinearassociation
2/cfg.fsample

** cfg.demean ** - ft_preprocessing, ft_resampledata
‘no’ or ‘yes’, whether to apply baseline correction (default = ‘no’)

** cfg.demean ** - ft_componentanalysis, ft_rejectcomponent
‘no’ or ‘yes’, whether to demean the input data (default = ‘yes’)

** cfg.demean ** - ft_mvaranalysis
‘yes’ (default) or ‘no’ explicit removal of DC-offset

** cfg.demean ** - ft_connectivitysimulation, ft_connectivitysimulation
‘yes’ (or ‘no’)

** cfg.demean ** - ft_combineplanar
‘yes’ or ‘no’ (default = ‘no’)

** cfg.demean ** - ft_channelnormalise
‘yes’ or ‘no’ (or boolean value) (default = ‘yes’)

** cfg.demeandata ** - ft_denoise_tsr
string, ‘yes’ or ‘no’, whether or not to make dependent variable zero mean prior to the regression (default = ‘no’)

** cfg.demeanrefdata ** - ft_denoise_tsr
string, ‘yes’ or ‘no’, whether or not to make reference data zero mean prior to the regression (default = ‘no’)

** cfg.density ** - ft_spike_plot_isireturn
‘yes’ or ‘no’, if ‘yes’, we will use color shading on top of the individual datapoints to indicate the density.

** cfg.derivative ** - ft_preprocessing
‘no’ or ‘yes’, computes the first order derivative of the data (default = ‘no’)

** cfg.design ** - ft_freqstatistics
Nxnumobservations: design matrix (for examples/advice, please see the FieldTrip wiki, especially cluster-permutation tutorial and the ‘walkthrough’ design-matrix section)

** cfg.detrend ** - ft_resampledata
‘no’ or ‘yes’, detrend the data prior to resampling (no default specified, see below)

** cfg.detrend ** - ft_preprocessing
‘no’ or ‘yes’, remove linear trend from the data (done per trial) (default = ‘no’)

** cfg.dewar ** - ft_realtime_headlocalizer
filename or mesh, description of the dewar shape (default is automatic)

** cfg.dftbandwidth ** - ft_preprocessing
bandwidth of line noise frequencies, applies to spectrum interpolation, in Hz (default = [1 2 3])

** cfg.dftfilter ** - ft_preprocessing
‘no’ or ‘yes’ line noise removal using discrete fourier transform (default = ‘no’)

** cfg.dftfreq ** - ft_preprocessing
line noise frequencies in Hz for DFT filter (default = [50 100 150])

** cfg.dftneighbourwidth ** - ft_preprocessing
bandwidth of frequencies neighbouring line noise frequencies, applies to spectrum interpolation, in Hz (default = [2 2 2])

** cfg.dftreplace ** - ft_preprocessing
‘zero’ or ‘neighbour’, method used to reduce line noise, ‘zero’ implies DFT filter, ‘neighbour’ implies spectrum interpolation (default = ‘zero’)

** cfg.dim ** - ft_volumereslice
[nx ny nz], size of the volume in each direction

** cfg.dim ** - ft_sliceinterp
integer value, default is 3 (dimension to slice)

** cfg.dip.amplitude ** - ft_dipolesimulation
per dipole

** cfg.dip.frequency ** - ft_dipolesimulation
in Hz

** cfg.dip.mom ** - ft_dipolesimulation
[Qx Qy Qz] (size 3xN)

** cfg.dip.phase ** - ft_dipolesimulation
in radians

** cfg.dip.pos ** - ft_dipolesimulation
[Rx Ry Rz] (size Nx3)

** cfg.dip.pos ** - ft_dipolefitting
initial dipole position, matrix of Ndipoles x 3

** cfg.dip.signal ** - ft_dipolesimulation

** cfg.dipfit.display ** - ft_dipolefitting
level of display, can be ‘off’, ‘iter’, ‘notify’ or ‘final’ (default = ‘iter’)

** cfg.dipfit.maxiter ** - ft_dipolefitting
maximum number of function evaluations allowed (default depends on the optimfun)

** cfg.dipfit.optimfun ** - ft_dipolefitting
function to use, can be ‘fminsearch’ or ‘fminunc’ (default is determined automatic)

** cfg.dipoleunit ** - ft_dipolesimulation
units for dipole amplitude (default nA*m)

** cfg.directionality ** - ft_multiplotTFR, ft_singleplotER, ft_singleplotTFR, ft_topoplotER, ft_topoplotTFR
‘’, ‘inflow’ or ‘outflow’ specifies for connectivity measures whether the inflow into a node, or the outflow from a node is plotted. The (default) behavior of this option depends on the dimor of the input data (see below).

** cfg.directionality ** - ft_multiplotER
‘’, ‘inflow’ or ‘outflow’ specifies for connectivity measures whether the inflow into a node, or the outflow from a node is plotted. The (default) behavior of this option depends on the dimord of the input data (see below).

** cfg.distmat ** - ft_sourceplot
precomputed distance matrix (default = [])

** cfg.downsample ** - ft_sourceplot
downsampling for resolution reduction, integer value (default = 1) (orig: from surface)

** cfg.downsample ** - ft_sourceinterpolate, ft_volumedownsample, ft_volumenormalise, ft_volumereslice, ft_volumewrite
integer number (default = 1, i.e. no downsampling)

** cfg.downsample ** - ft_prepare_mesh
integer number (default = 1, i.e. no downsampling), see FT_VOLUMEDOWNSAMPLE

** cfg.downsample ** - ft_volumesegment
integer, amount of downsampling before segmentation (default = 1; i.e., no downsampling)

** cfg.downscale ** - ft_spikesplitting
single number or vector (for each channel), corresponding to the number of bits removed from the LSB side (default = 0)

** cfg.dss.denf.function ** - ft_componentanalysis

** cfg.dss.denf.params ** - ft_componentanalysis

** cfg.dssp ** - ft_denoise_dssp
structure, containing the parameters that determine the behavior of the algorithm. cfg.dssp.n_space = ‘all’, or scalar. Number of dimensions for the initial spatial projection. cfg.dssp.n_in = ‘all’, or scalar. Number of dimensions of the subspace describing the field inside the ROI cfg.dssp.n_out = ‘all’, or scalar. Number of dimensions of the subspace describing the field outside the ROI cfg.dssp.n_intersect = scalar (default = 0.9). Number of dimensions (if value is an integer>=1), or threshold for the included eigenvalues (if value<1), determining the dimensionality of the intersection.

** cfg.dt ** - ft_spike_plot_isireturn
resolution of the 2-D histogram, or of the kernel plot in seconds. Since we have to smooth for a finite number of values, cfg.dt determines the resolution of our smooth density plot.

** cfg.duration ** - ft_steadystatesimulation
scalar, trial length in seconds (default = 4.56)

E

** cfg.ecgscale ** - ft_databrowser, ft_rejectvisual
number, scaling to apply to the ECG channels prior to display

** cfg.edgecolor ** - ft_sourceplot
[r g b] values or string, for example ‘brain’, ‘cortex’, ‘skin’, ‘black’, ‘red’, ‘r’

** cfg.eegscale ** - ft_databrowser, ft_rejectvisual
number, scaling to apply to the EEG channels prior to display

** cfg.elec ** - ft_prepare_headmodel

** cfg.elec ** - ft_electrodeplacement
struct containing previously placed electrodes (this overwrites cfg.channel)

** cfg.elec ** - ft_layoutplot, ft_neighbourplot, ft_scalpcurrentdensity
structure with electrode definition

** cfg.elec ** - ft_prepare_layout
structure with electrode definition, or

** cfg.elec ** - ft_channelrepair, ft_databrowser, ft_dipolefitting, ft_dipolesimulation, ft_electroderealign, ft_prepare_leadfield, ft_prepare_neighbours, ft_prepare_sourcemodel, ft_sourceanalysis
structure with electrode positions, see FT_DATATYPE_SENS

** cfg.elecfile ** - ft_prepare_headmodel
(required) string, filename of electrode configuration for the FEM leadfield

** cfg.elecfile ** - ft_layoutplot, ft_neighbourplot, ft_prepare_layout
filename containing electrode definition

** cfg.elecfile ** - ft_channelrepair, ft_databrowser, ft_dipolefitting, ft_dipolesimulation, ft_electroderealign, ft_prepare_leadfield, ft_prepare_neighbours, ft_prepare_sourcemodel, ft_sourceanalysis
name of file containing the electrode positions, see FT_READ_SENS

** cfg.elecfile ** - ft_scalpcurrentdensity
string, file containing the electrode definition

** cfg.emgscale ** - ft_databrowser, ft_rejectvisual
number, scaling to apply to the EMG channels prior to display

** cfg.ems ** - ft_mvaranalysis
‘no’ (default) or ‘yes’ explicit removal ensemble mean

** cfg.endsample ** - ft_redefinetrial
single number or Nx1 vector, expressed in samples relative to the start of the input trial

** cfg.envelopewindow ** - ft_heartrate, ft_respiration
scalar, time in seconds

** cfg.eogscale ** - ft_databrowser, ft_rejectvisual
number, scaling to apply to the EOG channels prior to display

** cfg.equalbinavg ** - ft_stratify
‘yes’

** cfg.errorbars ** - ft_spike_plot_psth
‘no’, ‘std’, ‘sem’ (default), ‘conf95%’ (requires statistic toolbox, according to student-T distribution), ‘var’

** cfg.errorbars ** - ft_spike_plot_raster
‘no’, ‘std’, ‘sem’ (default), ‘conf95%’,’var’

** cfg.eta ** - ft_sourcedescriptives
‘yes’ or ‘no’ (default = ‘no’)

** cfg.eventfile ** - ft_realtime_coillocalizer, ft_realtime_oddball, ft_realtime_ouunpod
string

** cfg.eventformat ** - ft_realtime_coillocalizer, ft_realtime_oddball, ft_realtime_ouunpod
string, default is determined automatic

** cfg.eventtype ** - ft_recodeevent
empty, ‘string’ or cell-array with multiple strings

** cfg.eventvalue ** - ft_recodeevent
empty or a list of event values (can be numeric or string)

F

** cfg.facecolor ** - ft_sourceplot
[r g b] values or string, for example ‘brain’, ‘cortex’, ‘skin’, ‘black’, ‘red’, ‘r’, or an Nx3 or Nx1 array where N is the number of faces

** cfg.fastica.a1 ** - ft_componentanalysis

** cfg.fastica.a2 ** - ft_componentanalysis

** cfg.fastica.approach ** - ft_componentanalysis

** cfg.fastica.dewhiteMat ** - ft_componentanalysis

** cfg.fastica.displayInterval ** - ft_componentanalysis

** cfg.fastica.displayMode ** - ft_componentanalysis

** cfg.fastica.epsilon ** - ft_componentanalysis

** cfg.fastica.finetune ** - ft_componentanalysis

** cfg.fastica.firstEig ** - ft_componentanalysis

** cfg.fastica.g ** - ft_componentanalysis

** cfg.fastica.initGuess ** - ft_componentanalysis

** cfg.fastica.interactivePCA ** - ft_componentanalysis

** cfg.fastica.lastEig ** - ft_componentanalysis

** cfg.fastica.maxFinetune ** - ft_componentanalysis

** cfg.fastica.maxNumIterations ** - ft_componentanalysis

** cfg.fastica.mu ** - ft_componentanalysis

** cfg.fastica.numOfIC ** - ft_componentanalysis

** cfg.fastica.only ** - ft_componentanalysis

** cfg.fastica.pcaD ** - ft_componentanalysis

** cfg.fastica.pcaE ** - ft_componentanalysis

** cfg.fastica.sampleSize ** - ft_componentanalysis

** cfg.fastica.stabilization ** - ft_componentanalysis

** cfg.fastica.verbose ** - ft_componentanalysis

** cfg.fastica.whiteMat ** - ft_componentanalysis

** cfg.fastica.whiteSig ** - ft_componentanalysis

** cfg.feedback ** - ft_megplanar

** cfg.feedback ** - ft_defacevolume
‘no’ or ‘yes’, whether to provide graphical feedback (default = ‘no’)

** cfg.feedback ** - ft_sourcedescriptives
‘no’, ‘text’ (default), ‘textbar’, ‘gui’

** cfg.feedback ** - ft_spiketriggeredaverage, ft_spiketriggeredinterpolation, ft_spiketriggeredspectrum_fft
‘no’, ‘text’, ‘textbar’, ‘gui’ (default = ‘no’)

** cfg.feedback ** - ft_componentanalysis, ft_resampledata, ft_sourceanalysis
‘no’, ‘text’, ‘textbar’, ‘gui’ (default = ‘text’)

** cfg.feedback ** - ft_spikesorting
‘no’, ‘text’, ‘textbar’, ‘gui’ (default = ‘textbar’)

** cfg.feedback ** - ft_freqanalysis_mvar
‘none’, or any of the methods supported by FT_PROGRESS, for providing feedback to the user in the command window.

** cfg.feedback ** - ft_electrodermalactivity, ft_heartrate, ft_respiration
‘yes’ or ‘no’

** cfg.feedback ** - ft_electroderealign, ft_prepare_neighbours
‘yes’ or ‘no’ (default = ‘no’)

** cfg.feedback ** - ft_electroderealign
‘yes’ or ‘no’ (default), feedback of the iteration procedure

** cfg.feedback ** - ft_prepare_headmodel
(optional)

** cfg.feedback ** - ft_topoplotCC
string (default = ‘textbar’)

** cfg.feedback ** - ft_statistics_montecarlo
string, ‘gui’, ‘text’, ‘textbar’ or ‘no’ (default = ‘text’)

** cfg.feedback ** - ft_statistics_stats
string, ‘gui’, ‘text’, ‘textbar’ or ‘no’ (default = ‘textbar’)

** cfg.feedback ** - ft_analysispipeline
string, ‘no’, ‘text’, ‘gui’ or ‘yes’, whether text and/or graphical feedback should be presented (default = ‘yes’)

** cfg.feedback ** - ft_interpolatenan, ft_scalpcurrentdensity
string, ‘no’, ‘text’, ‘textbar’, ‘gui’ (default = ‘text’)

** cfg.feedback ** - ft_spikesplitting
string, (default = ‘textbar’)

** cfg.feedback ** - ft_electrodeplacement
string, can be ‘yes’ or ‘no’ for detailled feedback (default = ‘yes’)

** cfg.feedback ** - ft_connectivityanalysis
string, specifying the feedback presented to the user. Default is ‘none’. See FT_PROGRESS

** cfg.fiducial ** - ft_electroderealign
cell-array with the name of three fiducials used for realigning (default = {‘nasion’, ‘lpa’, ‘rpa’})

** cfg.fiducial.ac ** - ft_volumerealign
[i j k], position of anterior commissure

** cfg.fiducial.ini ** - ft_electrodeplacement
1x3 vector with coordinates

** cfg.fiducial.lpa ** - ft_electrodeplacement
1x3 vector with coordinates

** cfg.fiducial.lpa ** - ft_volumerealign
[i j k], position of LPA

** cfg.fiducial.lpa ** - ft_volumewrite
[x y z] position of LPA

** cfg.fiducial.lpa ** - ft_meshrealign
[x y z], position of LPA

** cfg.fiducial.nas ** - ft_electrodeplacement
1x3 vector with coordinates

** cfg.fiducial.nas ** - ft_volumerealign
[i j k], position of nasion

** cfg.fiducial.nas ** - ft_volumewrite
[x y z] position of nasion

** cfg.fiducial.nas ** - ft_meshrealign
[x y z], position of nasion

** cfg.fiducial.pc ** - ft_volumerealign
[i j k], position of posterior commissure

** cfg.fiducial.rpa ** - ft_electrodeplacement
1x3 vector with coordinates

** cfg.fiducial.rpa ** - ft_volumerealign
[i j k], position of RPA

** cfg.fiducial.rpa ** - ft_volumewrite
[x y z] position of RPA

** cfg.fiducial.rpa ** - ft_meshrealign
[x y z], position of RPA

** cfg.fiducial.xzpoint ** - ft_volumerealign
[i j k], point on the midsagittal-plane with a positive Z-coordinate, i.e. an interhemispheric point above ac and pc

** cfg.fiducial.zpoint ** - ft_volumerealign
[i j k], a point on the positive z-axis. This is an optional ‘fiducial’, and can be used to determine whether the input voxel coordinate axes are left-handed (i.e. flipped in one of the dimensions). If this additional point is specified, and the voxel coordinate axes are left handed, the volume is flipped to yield right handed voxel axes.

** cfg.figurename ** - ft_sourceplot
string, title of the figure window

** cfg.filename ** - ft_volumewrite
filename without the extension

** cfg.filename ** - ft_analysispipeline, ft_sourcewrite
string, filename without the extension

** cfg.filetype ** - ft_volumewrite
‘analyze’, ‘nifti’, ‘nifti_img’, ‘analyze_spm’, ‘mgz’, ‘vmp’ or ‘vmr’

** cfg.filetype ** - ft_analysispipeline
string, can be ‘matlab’, ‘html’ or ‘dot’

** cfg.filetype ** - ft_sourcewrite
string, can be ‘nifti’, ‘gifti’ or ‘cifti’ (default is automatic)

** cfg.fitind ** - ft_prepare_headmodel
(optional)

** cfg.fixedori ** - ft_sourcedescriptives
‘within_trials’ or ‘over_trials’ (default = ‘over_trials’)

** cfg.flank.mindist ** - ft_spikedetection
mininum distance in samples between detected peaks

** cfg.flank.offset ** - ft_spikedetection
number of samples before peak

** cfg.flank.value ** - ft_spikedetection
positive or negative threshold

** cfg.flank.ztransform ** - ft_spikedetection
‘yes’ or ‘no’

** cfg.flipdim ** - ft_sliceinterp
flip data along the sliced dimension, ‘yes’ or ‘no’ (default = ‘no’)

** cfg.foi ** - ft_topoplotCC
the frequency of interest which is to be plotted (default is the first frequency bin)

** cfg.foi ** - ft_freqanalysis
vector 1 x numfoi, frequencies of interest

** cfg.foi ** - ft_freqanalysis, ft_freqanalysis
vector 1 x numfoi, frequencies of interest OR

** cfg.foi ** - ft_freqanalysis_mvar
vector with the frequencies at which the spectral quantities are estimated (in Hz). Default: 0:1:Nyquist

** cfg.foilim ** - ft_freqinterpolate
Nx2 matrix with begin and end of each interval to be interpolated (default = [49 51; 99 101; 149 151])

** cfg.foilim ** - ft_realtime_ouunpod
[Flow Fhigh] (default = [1 45])

** cfg.foilim ** - ft_freqanalysis, ft_freqanalysis
[begin end], frequency band of interest

** cfg.foilim ** - ft_spiketriggeredspectrum_fft
[begin end], frequency band of interest (default = [0 150])

** cfg.foilim ** - ft_freqanalysis
[begin end], frequency band of interest OR

** cfg.foilim ** - ft_freqgrandaverage
[fmin fmax] or ‘all’, to specify a subset of frequencies (default = ‘all’)

** cfg.fontsize ** - ft_multiplotER
font size of comment and labels (default = 8)

** cfg.fontsize ** - ft_multiplotTFR
font size of comment and labels (if present) (default = 8)

** cfg.fontsize ** - ft_singleplotER, ft_singleplotTFR
font size of title (default = 8)

** cfg.fontsize ** - ft_databrowser
number, fontsize inside the figure (default = 0.03)

** cfg.fontunits ** - ft_databrowser
string, can be ‘normalized’, ‘points’, ‘pixels’, ‘inches’ or ‘centimeters’ (default = ‘normalized’)

** cfg.fontweight ** - ft_multiplotTFR
font weight of comment and labels (if present)

** cfg.format ** - ft_spikesplitting
‘int16’ or ‘int32’ (default = ‘int32’)

** cfg.framesfile ** - ft_movieplotTFR
[] (optional), no file saved, or ‘string’, filename of saved frames.mat (default = []);

** cfg.framesfile ** - ft_movieplotER
[], no file saved, or ‘string’, filename of saved frames.mat (default = []);

** cfg.framespersec ** - ft_movieplotER, ft_movieplotTFR
number, frames per second (default = 5)

** cfg.freqhigh ** - ft_crossfrequencyanalysis
scalar or vector, selection of frequencies for the high frequency data

** cfg.freqlow ** - ft_crossfrequencyanalysis
scalar or vector, selection of frequencies for the low frequency data

** cfg.frequency ** - ft_freqstatistics
[begin end], can be ‘all’ (default = ‘all’)

** cfg.frequency ** - ft_freqdescriptives
[fmin fmax] or ‘all’, to specify a subset of frequencies (default = ‘all’)

** cfg.frequency ** - ft_sourceplot
scalar or string, can be ‘all’, or [beg end], specify frequency range in Hz

** cfg.frequency ** - ft_dipolefitting, ft_sourceanalysis
single number (in Hz)

** cfg.fsample ** - ft_nonlinearassociation
1200

** cfg.fsample ** - ft_spikedensity
additional user input that can be used when input is a SPIKE structure, in that case a continuous representation is created using cfg.fsample (default = 1000)

** cfg.fsample ** - ft_spikedownsample
desired sampling frequency in Hz (default = 1000)

** cfg.fsample ** - ft_connectivitysimulation
in Hz

** cfg.fsample ** - ft_dipolesimulation
sampling frequency in Hz

** cfg.fsample ** - ft_spike_waveform
sampling frequency of waveform time-axis. Obligatory field.

** cfg.fsample ** - ft_steadystatesimulation
scalar, sampling frequency in Hz (default = 512)

** cfg.fsample ** - ft_freqsimulation
simulated sample frequency

** cfg.fsample ** - ft_timelocksimulation
simulated sample frequency (default = 1000)

** cfg.fshome ** - ft_prepare_mesh
‘/path/to/freesurfer dir’; cortex_hull = ft_prepare_mesh(cfg);

** cfg.fshome ** - ft_electroderealign
string, path to freesurfer

** cfg.fsl.costfun ** - ft_volumerealign
string, specifying the cost-function used for coregistration

** cfg.fsl.dof ** - ft_volumerealign
scalar, specifying the number of parameters for the affine transformation. 6 (rigid body), 7 (global rescale), 9 (traditional) or 12.

** cfg.fsl.interpmethod ** - ft_volumerealign
string, specifying the interpolation method, can be ‘trilinear’, ‘nearestneighbour’, or ‘sinc’

** cfg.fsl.path ** - ft_volumerealign
string, specifying the path to fsl

** cfg.fsl.reslice ** - ft_volumerealign
string, specifying whether the output image will be resliced conform the target image (default = ‘yes’)

** cfg.funcolorlim ** - ft_sourceplot
color range of the functional data (default = ‘auto’) [min max] ‘maxabs’, from -max(abs(funparameter)) to +max(abs(funparameter)) ‘zeromax’, from 0 to max(funparameter) ‘minzero’, from min(funparameter) to 0 ‘auto’, if funparameter values are all positive: ‘zeromax’, all negative: ‘minzero’, both possitive and negative: ‘maxabs’

** cfg.funcolormap ** - ft_sourceplot
colormap for functional data, see COLORMAP (default = ‘auto’) ‘auto’, depends structure funparameter, or on funcolorlim - funparameter: only positive values, or funcolorlim:’zeromax’ -> ‘hot’ - funparameter: only negative values, or funcolorlim:’minzero’ -> ‘cool’ - funparameter: both pos and neg values, or funcolorlim:’maxabs’ -> ‘default’ - funcolorlim: [min max] if min & max pos-> ‘hot’, neg-> ‘cool’, both-> ‘default’

** cfg.funparameter ** - ft_sliceinterp
string with the functional parameter of interest (default = ‘source’)

** cfg.funparameter ** - ft_sourceplot
string, field in data with the functional parameter of interest (default = [])

** cfg.funparameter ** - ft_sourcemovie
string, functional parameter that is color coded (default = ‘avg.pow’)

G

** cfg.gaussvar ** - ft_spike_plot_isireturn, ft_spike_plot_jpsth
variance (default = 1/16 of window length in sec).

** cfg.grad ** - ft_prepare_headmodel, ft_prepare_headmodel

** cfg.grad ** - ft_layoutplot, ft_neighbourplot
structure with gradiometer definition

** cfg.grad ** - ft_prepare_layout
structure with gradiometer definition, or

** cfg.grad ** - ft_channelrepair, ft_databrowser, ft_dipolefitting, ft_dipolesimulation, ft_prepare_leadfield, ft_prepare_neighbours, ft_prepare_sourcemodel, ft_sourceanalysis
structure with gradiometer definition, see FT_DATATYPE_SENS

** cfg.gradfile ** - ft_layoutplot, ft_neighbourplot, ft_prepare_layout
filename containing gradiometer definition

** cfg.gradfile ** - ft_channelrepair, ft_databrowser, ft_dipolefitting, ft_dipolesimulation, ft_prepare_leadfield, ft_prepare_neighbours, ft_prepare_sourcemodel, ft_sourceanalysis
name of file containing the gradiometer definition, see FT_READ_SENS

** cfg.gradient ** - ft_denoise_synthetic
‘none’, ‘G1BR’, ‘G2BR’ or ‘G3BR’ specifies the gradiometer type to which the data should be changed

** cfg.gradscale ** - ft_multiplotER, ft_multiplotTFR
number, scaling to apply to the MEG gradiometer channels prior to display

** cfg.gradscale ** - ft_databrowser, ft_rejectvisual
number, scaling to apply to the MEG gradiometer channels prior to display (in addition to the cfg.megscale factor)

** cfg.graphcolor ** - ft_multiplotER
color(s) used for plotting the dataset(s) (default = ‘brgkywrgbkywrgbkywrgbkyw’) alternatively, colors can be specified as Nx3 matrix of RGB values

** cfg.graphcolor ** - ft_singleplotER
color(s) used for plotting the dataset(s) (default = ‘brgkywrgbkywrgbkywrgbkyw’) alternatively, colors can be specified as nx3 matrix of rgb values

** cfg.grid ** - ft_dipolefitting, ft_sourceanalysis
structure, see FT_PREPARE_SOURCEMODEL or FT_PREPARE_LEADFIELD

** cfg.grid ** - ft_denoise_dssp
structure, source model with precomputed leadfields (see FT_PREPARE_LEADFIELD)

** cfg.grid.corner1 ** - ft_electrodeplacement
1x3 position of the upper left corner point

** cfg.grid.corner2 ** - ft_electrodeplacement
1x3 position of the upper right corner point

** cfg.grid.corner3 ** - ft_electrodeplacement
1x3 position of the lower left corner point

** cfg.grid.corner4 ** - ft_electrodeplacement
1x3 position of the lower right corner point

** cfg.grid.dim ** - ft_dipolefitting, ft_prepare_leadfield, ft_sourceanalysis
[Nx Ny Nz] vector with dimensions in case of 3-D grid (optional)

** cfg.grid.dim ** - ft_prepare_sourcemodel
[Nx Ny Nz] vector with dimensions in case of 3D grid (optional)

** cfg.grid.filter ** - ft_sourceanalysis

** cfg.grid.filter ** - ft_prepare_sourcemodel
or alternatively cfg.grid.avg.filter

** cfg.grid.inside ** - ft_dipolefitting, ft_prepare_leadfield, ft_prepare_sourcemodel, ft_sourceanalysis
N*1 vector with boolean value whether grid point is inside brain (optional)

** cfg.grid.lbex ** - ft_prepare_sourcemodel

** cfg.grid.leadfield ** - ft_prepare_sourcemodel, ft_sourceanalysis

** cfg.grid.nonlinear ** - ft_prepare_sourcemodel
‘no’ (or ‘yes’), use non-linear normalization

** cfg.grid.pos ** - ft_dipolefitting, ft_prepare_leadfield, ft_prepare_sourcemodel, ft_sourceanalysis
N*3 matrix with position of each source

** cfg.grid.pos ** - ft_dipolefitting, ft_sourceanalysis
N*3 matrix with the vertex positions of the cortical sheet

** cfg.grid.resolution ** - ft_dipolefitting, ft_prepare_leadfield, ft_prepare_sourcemodel, ft_sourceanalysis
number (e.g. 1 cm) for automatic grid generation

** cfg.grid.resolution ** - ft_prepare_sourcemodel
number (e.g. 6) of the resolution of the template MNI grid, defined in mm

** cfg.grid.subspace ** - ft_prepare_sourcemodel

** cfg.grid.template ** - ft_prepare_sourcemodel
specification of a template grid (grid structure), or a filename of a template grid (defined in MNI space), either cfg.grid.resolution or cfg.grid.template needs to be defined. If both are defined cfg.grid.template prevails

** cfg.grid.tight ** - ft_prepare_sourcemodel
‘yes’ or ‘no’ (default is automatic)

** cfg.grid.tri ** - ft_dipolefitting, ft_sourceanalysis
M*3 matrix that describes the triangles connecting the vertices

** cfg.grid.unit ** - ft_prepare_sourcemodel
string, can be ‘mm’, ‘cm’, ‘m’ (default is automatic)

** cfg.grid.warpmni ** - ft_prepare_sourcemodel
‘yes’

** cfg.grid.xgrid ** - ft_dipolefitting, ft_prepare_leadfield, ft_prepare_sourcemodel, ft_sourceanalysis
vector (e.g. -20:1:20) or ‘auto’ (default = ‘auto’)

** cfg.grid.ygrid ** - ft_dipolefitting, ft_prepare_leadfield, ft_prepare_sourcemodel, ft_sourceanalysis
vector (e.g. -20:1:20) or ‘auto’ (default = ‘auto’)

** cfg.grid.zgrid ** - ft_dipolefitting, ft_prepare_leadfield, ft_prepare_sourcemodel, ft_sourceanalysis
vector (e.g. 0:1:20) or ‘auto’ (default = ‘auto’)

** cfg.gridscale ** - ft_topoplotER, ft_topoplotIC, ft_topoplotTFR
scaling grid size (default = 67) determines resolution of figure

** cfg.gridsearch ** - ft_dipolefitting
‘yes’ or ‘no’, perform global search for initial guess for the dipole parameters (default = ‘yes’)

** cfg.gwidth ** - ft_freqanalysis, ft_freqanalysis
determines the length of the used wavelets in standard deviations of the implicit Gaussian kernel and should be choosen >= 3; (default = 3)

H

** cfg.hdr ** - ft_spike_maketrials
struct, should be specified if cfg.trlunit = ‘samples’. This should be specified as cfg.hdr = data.hdr where data.hdr contains the subfields data.hdr.Fs (sampling frequency of the LFP), data.hdr.FirstTimeStamp, and data.hdr.TimeStampPerSecond.

** cfg.headerfile ** - ft_realtime_coillocalizer, ft_realtime_oddball, ft_realtime_ouunpod
string

** cfg.headerfile ** - ft_artifact_clip, ft_artifact_ecg, ft_artifact_eog, ft_artifact_jump, ft_artifact_muscle, ft_artifact_threshold, ft_artifact_tms, ft_artifact_zvalue, ft_databrowser, ft_preprocessing
string with the filename

** cfg.headerformat ** - ft_artifact_ecg, ft_artifact_eog, ft_artifact_jump, ft_artifact_muscle, ft_artifact_threshold, ft_artifact_tms, ft_artifact_zvalue

** cfg.headerformat ** - ft_realtime_coillocalizer, ft_realtime_oddball, ft_realtime_ouunpod
string, default is determined automatic

** cfg.headmodel ** - ft_prepare_headmodel
(required) string, filename of precomputed FEM leadfield

** cfg.headmodel ** - ft_dipolefitting, ft_dipolesimulation, ft_megplanar, ft_prepare_leadfield, ft_prepare_sourcemodel, ft_sourceanalysis
structure with volume conduction model, see FT_PREPARE_HEADMODEL

** cfg.headmodel ** - ft_megrealign
structure, see FT_PREPARE_HEADMODEL

** cfg.headmovement ** - ft_realtime_headlocalizer
string, name or location of the .pos file created by MaxFilter which describes the location of the head relative to the dewar

** cfg.headshape ** - ft_prepare_mesh
‘/path/to/surf/lh.pial’;

** cfg.headshape ** - ft_prepare_mesh
a filename containing headshape, a Nx3 matrix with surface points, or a structure with a single or multiple boundaries

** cfg.headshape ** - ft_electroderealign, ft_electroderealign, ft_megplanar, ft_megrealign
a filename containing headshape, a structure containing a single triangulated boundary, or a Nx3 matrix with surface points

** cfg.headshape ** - ft_prepare_sourcemodel
a filename for the headshape, a structure containing a single surface, or a Nx3 matrix with headshape surface points (default = [])

** cfg.headshape ** - ft_realtime_headlocalizer
filename or mesh, description of the head shape recorded with the Structure Sensor

** cfg.headshape ** - ft_prepare_mesh
sting, filename containing the pial surface computed by freesurfer recon-all

** cfg.headshape ** - ft_electroderealign
string, filename containing subject headshape (e.g. <path to freesurfer/surf/lh.pial>)

** cfg.headshape ** - ft_prepare_sourcemodel
string, should be a *.fif file

** cfg.headshape ** - ft_prepare_layout
surface mesh (e.g. pial, head, etc) to be used for generating an outline, see FT_READ_HEADSHAPE for details

** cfg.headshape.headshape ** - ft_volumerealign
string pointing to a file describing a headshape or a FieldTrip-structure describing a headshape, see FT_READ_HEADSHAPE

** cfg.headshape.icp ** - ft_volumerealign
‘yes’ or ‘no’, use automatic realignment based on the icp-algorithm. If both ‘interactive’ and ‘icp’ are executed, the icp step follows the interactive realignment step (default = ‘yes’)

** cfg.headshape.interactive ** - ft_volumerealign
‘yes’ or ‘no’, use interactive realignment to align headshape with scalp surface (default = ‘yes’)

** cfg.headshape.scalpsmooth ** - ft_volumerealign
scalar, smoothing parameter for the scalp extraction (default = 2)

** cfg.headshape.scalpthreshold ** - ft_volumerealign
scalar, threshold parameter for the scalp extraction (default = 0.1)

** cfg.highlight ** - ft_topoplotER, ft_topoplotTFR
‘off’, ‘on’, ‘labels’, ‘numbers’

** cfg.highlight ** - ft_topoplotIC
‘on’, ‘labels’, ‘numbers’, ‘off’

** cfg.highlightchannel ** - ft_topoplotER, ft_topoplotIC, ft_topoplotTFR
Nx1 cell-array with selection of channels, or vector containing channel indices see FT_CHANNELSELECTION

** cfg.highlightcolor ** - ft_topoplotER, ft_topoplotIC, ft_topoplotTFR
highlight marker color (default = [0 0 0] (black))

** cfg.highlightcolorneg ** - ft_clusterplot
color of highlight marker for negative clusters (default = [0 0 0])

** cfg.highlightcolorpos ** - ft_clusterplot
color of highlight marker for positive clusters (default = [0 0 0])

** cfg.highlightfontsize ** - ft_topoplotER, ft_topoplotIC, ft_topoplotTFR
highlight marker size (default = 8)

** cfg.highlightseries ** - ft_clusterplot
1x5 cell-array, highlight option series with ‘on’, ‘labels’ or ‘numbers’ (default {‘on’, ‘on’, ‘on’, ‘on’, ‘on’} for p < [0.01 0.05 0.1 0.2 0.3]

** cfg.highlightsize ** - ft_topoplotER, ft_topoplotIC, ft_topoplotTFR
highlight marker size (default = 6)

** cfg.highlightsizeseries ** - ft_clusterplot
1x5 vector, highlight marker size series (default [6 6 6 6 6] for p < [0.01 0.05 0.1 0.2 0.3])

** cfg.highlightsymbol ** - ft_topoplotER, ft_topoplotIC, ft_topoplotTFR
highlight marker symbol (default = ‘o’)

** cfg.highlightsymbolseries ** - ft_clusterplot
1x5 vector, highlight marker symbol series (default [‘*’, ‘x’, ‘+’, ‘o’, ‘.’] for p < [0.01 0.05 0.1 0.2 0.3]

** cfg.hilbert ** - ft_preprocessing
‘no’, ‘abs’, ‘complex’, ‘real’, ‘imag’, ‘absreal’, ‘absimag’ or ‘angle’ (default = ‘no’)

** cfg.hotkeys ** - ft_singleplotER
enables hotkeys (leftarrow/rightarrow/uparrow/downarrow/m) for dynamic zoom and translation (ctrl+) of the axes

** cfg.hotkeys ** - ft_singleplotTFR
enables hotkeys (leftarrow/rightarrow/uparrow/downarrow/pageup/pagedown/m) for dynamic zoom and translation (ctrl+) of the axes and color limits

** cfg.hotkeys ** - ft_topoplotER, ft_topoplotTFR
enables hotkeys (pageup/pagedown/m) for dynamic zoom and translation (ctrl+) of the color limits

** cfg.hotkeys ** - ft_multiplotTFR
enables hotkeys (up/down arrows) for dynamic colorbar adjustment

** cfg.hpfiltdev ** - ft_preprocessing
highpass max passband deviation (firws with ‘kaiser’ window, default 0.001 set in low-level function)

** cfg.hpfiltdf ** - ft_preprocessing
highpass transition width (firws, overrides order, default set in low-level function)

** cfg.hpfiltdir ** - ft_preprocessing
filter direction, ‘twopass’ (default), ‘onepass’ or ‘onepass-reverse’ or ‘onepass-zerophase’ (default for firws) or ‘onepass-minphase’ (firws, non-linear!)

** cfg.hpfilter ** - ft_preprocessing
‘no’ or ‘yes’ highpass filter (default = ‘no’)

** cfg.hpfiltord ** - ft_preprocessing
highpass filter order (default set in low-level function)

** cfg.hpfilttype ** - ft_preprocessing
digital filter type, ‘but’ or ‘firws’ or ‘fir’ or ‘firls’ (default = ‘but’)

** cfg.hpfiltwintype ** - ft_preprocessing
highpass window type, ‘hann’ or ‘hamming’ (default) or ‘blackman’ or ‘kaiser’ (firws)

** cfg.hpfreq ** - ft_preprocessing
highpass frequency in Hz

** cfg.hpinstabilityfix ** - ft_preprocessing
deal with filter instability, ‘no’, ‘reduce’, ‘split’ (default = ‘no’)

I

** cfg.icasso.Niter ** - ft_componentanalysis

** cfg.icasso.mode ** - ft_componentanalysis

** cfg.image ** - ft_prepare_layout
filename, use an image to construct a layout (e.g. useful for ECoG grids)

** cfg.image ** - ft_layoutplot
filename, use an image to construct a layout (e.g. usefull for ECoG grids)

** cfg.implicitref ** - ft_preprocessing
‘label’ or empty, add the implicit EEG reference as zeros (default = [])

** cfg.implicitref ** - ft_prepare_montage
string with the label of the implicit reference, or empty (default = [])

** cfg.individual.elec ** - ft_interactiverealign
structure

** cfg.individual.grad ** - ft_interactiverealign
structure

** cfg.individual.headmodel ** - ft_interactiverealign
structure, see FT_PREPARE_HEADMODEL

** cfg.individual.headmodelstyle ** - ft_interactiverealign
‘vertex’, ‘edge’, ‘surface’ or ‘both’ (default = ‘edge’)

** cfg.individual.headshape ** - ft_interactiverealign
structure, see FT_READ_HEADSHAPE

** cfg.individual.headshapestyle ** - ft_interactiverealign
‘vertex’, ‘edge’, ‘surface’ or ‘both’ (default = ‘vertex’)

** cfg.individual.mri ** - ft_interactiverealign
structure, see FT_READ_MRI

** cfg.input ** - ft_omri_pipeline, ft_omri_pipeline_nuisance
FieldTrip buffer containing raw scans (default ‘buffer://localhost:1972’)

** cfg.input ** - ft_omri_quality
FieldTrip buffer containing raw scans (default=’buffer://localhost:1972’)

** cfg.inputcoord ** - ft_volumelookup, ft_volumelookup, ft_volumelookup
‘mni’ or ‘tal’, coordinate system of the mri/source/stat

** cfg.inputfile ** - ft_analysispipeline, ft_annotate, ft_anonymizedata, ft_appenddata, ft_appendfreq, ft_artifact_clip, ft_artifact_ecg, ft_artifact_eog, ft_artifact_jump, ft_artifact_muscle, ft_artifact_nan, ft_artifact_threshold, ft_artifact_tms, ft_channelnormalise, ft_channelrepair, ft_clusterplot, ft_combineplanar, ft_componentanalysis, ft_connectivityanalysis, ft_denoise_synthetic, ft_detect_movement, ft_dipolefitting, ft_examplefunction, ft_freqanalysis, ft_freqanalysis_mvar, ft_freqdescriptives, ft_freqgrandaverage, ft_freqinterpolate, ft_freqstatistics, ft_globalmeanfield, ft_interpolatenan, ft_lateralizedpotential, ft_layoutplot, ft_math, ft_megplanar, ft_megrealign, ft_meshrealign, ft_movieplotER, ft_movieplotTFR, ft_multiplotER, ft_multiplotTFR, ft_mvaranalysis, ft_networkanalysis, ft_prepare_leadfield, ft_prepare_mesh, ft_preprocessing, ft_redefinetrial, ft_regressconfound, ft_rejectartifact, ft_rejectcomponent, ft_rejectvisual, ft_removetemplateartifact, ft_resampledata, ft_scalpcurrentdensity, ft_singleplotER, ft_sourceanalysis, ft_sourcedescriptives, ft_sourcegrandaverage, ft_sourceinterpolate, ft_sourcemovie, ft_sourceplot, ft_sourcewrite, ft_timelockanalysis, ft_timelockbaseline, ft_timelockgrandaverage, ft_timelockstatistics, ft_topoplotCC, ft_topoplotTFR, ft_volumedownsample, ft_volumenormalise, ft_volumerealign, ft_volumereslice, ft_volumesegment, ft_volumewrite

** cfg.interactive ** - ft_movieplotTFR
‘no’ or ‘yes’, make it interactive

** cfg.interactive ** - ft_spike_plot_raster
‘yes’ (default) or ‘no’. If ‘yes’, zooming and panning operate via callbacks.

** cfg.interactive ** - ft_spikedetection
‘yes’ or ‘no’

** cfg.interactive ** - ft_audiovideobrowser
‘yes’ or ‘no’ (default = ‘yes’)

** cfg.interactive ** - ft_sliceinterp
‘yes’ or ‘no’ (default), interactive coordinates and source values

** cfg.interactive ** - ft_multiplotER
‘yes’ or ‘no’, make the plot interactive (default = ‘yes’) In a interactive plot you can select areas and produce a new interactive plot when a selected area is clicked. Multiple areas can be selected by holding down the SHIFT key.

** cfg.interactive ** - ft_multiplotTFR, ft_singleplotTFR, ft_topoplotER, ft_topoplotTFR
Interactive plot ‘yes’ or ‘no’ (default = ‘yes’) In a interactive plot you can select areas and produce a new interactive plot when a selected area is clicked. Multiple areas can be selected by holding down the SHIFT key.

** cfg.interactive ** - ft_singleplotER
interactive plot ‘yes’ or ‘no’ (default = ‘yes’) in a interactive plot you can select areas and produce a new interactive plot when a selected area is clicked. multiple areas can be selected by holding down the shift key.

** cfg.interplimits ** - ft_topoplotER, ft_topoplotIC, ft_topoplotTFR
limits for interpolation (default = ‘head’) ‘electrodes’ to furthest electrode ‘head’ to edge of head

** cfg.interpmethod ** - ft_sourceinterpolate
string, can be ‘nearest’, ‘linear’, ‘cubic’, ‘spline’, ‘sphere_avg’ or ‘smudge’ (default = ‘linear for interpolating two 3D volumes, ‘nearest’ for all other cases)

** cfg.interpolate ** - ft_spike_waveform
double integer (default = 1). Increaes the density of samples by a factor cfg.interpolate

** cfg.interpolate ** - ft_spike_plot_isireturn, ft_spike_plot_jpsth
integer (default = 1), we perform interpolating with extra number of spacings determined by cfg.interpolate. For example cfg.interpolate = 5 means 5 times more dense axis.

** cfg.interpolatenan ** - ft_topoplotER, ft_topoplotTFR
string ‘yes’, ‘no’ (default = ‘yes’) interpolate over channels containing NaNs

** cfg.interpolation ** - ft_topoplotER, ft_topoplotIC, ft_topoplotTFR
‘linear’,’cubic’,’nearest’,’v4’ (default = ‘v4’) see GRIDDATA

** cfg.interptoi ** - ft_spiketriggeredinterpolation
value, time in seconds used for interpolation, which must be larger than timwin (default = 0.2)

** cfg.inwardshift ** - ft_megrealign

** cfg.inwardshift ** - ft_megplanar
depth of the source layer relative to the head model surface (default = 2.5 cm, which is appropriate for a skin-based head model)

** cfg.inwardshift ** - ft_megrealign
depth of the source layer relative to the headshape surface or volume conduction model (no default supplied, see below)

** cfg.inwardshift ** - ft_prepare_sourcemodel
number, how much should the innermost surface be moved inward to constrain sources to be considered inside the source compartment (default = 0)

** cfg.isolatedsource ** - ft_prepare_headmodel
(optional)

** cfg.iti ** - ft_steadystatesimulation
scalar, inter-trial interval in seconds (default = 1)

** cfg.ivar ** - ft_statistics_analytic, ft_statistics_montecarlo
number or list with indices, independent variable(s)

J

** cfg.jackknife ** - ft_mvaranalysis
‘no’ (default) or ‘yes’ specifies whether the coefficients are estimated for all leave-one-out sets of trials

** cfg.jackknife ** - ft_sourceanalysis
‘no’ or ‘yes’ jackknife resampling of trials

** cfg.jackknife ** - ft_freqdescriptives
‘yes’ or ‘no’, estimate standard error by means of the jack-knife (default = ‘no’)

** cfg.jumptoeof ** - ft_realtime_coillocalizer
causes the realtime function to jump to the end

** cfg.jumptoeof ** - ft_realtime_coillocalizer
whether to skip to the end of the stream/file at startup (default = ‘yes’)

K

** cfg.keepbrain ** - ft_defacevolume
‘no’ or ‘yes’, segment and retain the brain (default = ‘no’)

** cfg.keepchannel ** - ft_electroderealign
string, ‘yes’ or ‘no’ (default = ‘no’)

** cfg.keepchannel ** - ft_rejectvisual
string, determines how to deal with channels that are not selected, can be ‘no’ completely remove deselected channels from the data (default) ‘yes’ keep deselected channels in the output data ‘nan’ fill the channels that are deselected with NaNs ‘repair’ repair the deselected channels using FT_CHANNELREPAIR

** cfg.keepcsd ** - ft_sourceanalysis
‘no’ or ‘yes’

** cfg.keepcsd ** - ft_sourcedescriptives
‘yes’ or ‘no’ (default = ‘no’)

** cfg.keepfield ** - ft_anonymizedata
cell-array with strings, fields to keep (default = {})

** cfg.keepfilter ** - ft_sourceanalysis
‘no’ or ‘yes’

** cfg.keepindividual ** - ft_sourcegrandaverage
‘no’ or ‘yes’

** cfg.keepindividual ** - ft_freqgrandaverage, ft_timelockgrandaverage
‘yes’ or ‘no’ (default = ‘no’)

** cfg.keepinside ** - ft_volumedownsample
‘yes’ or ‘no’, keep the inside/outside labeling (default = ‘yes’)

** cfg.keepleadfield ** - ft_sourceanalysis
‘no’ or ‘yes’

** cfg.keepmom ** - ft_sourceanalysis
‘no’ or ‘yes’

** cfg.keepmom ** - ft_sourcedescriptives
‘yes’ or ‘no’ (default = ‘yes’)

** cfg.keepnoisecsd ** - ft_sourcedescriptives
‘yes’ or ‘no’ (default = ‘no’)

** cfg.keepnoisemom ** - ft_sourcedescriptives
‘yes’ or ‘no’ (default = ‘yes’)

** cfg.keepnumeric ** - ft_anonymizedata
‘yes’ or ‘no’, keep numeric fields (default = ‘yes’)

** cfg.keepremoved ** - ft_analysispipeline
‘yes’ or ‘no’, determines whether removed fields are completely removed, or only replaced by a short textual description (default = ‘no’)

** cfg.keepsampleinfo ** - ft_appenddata, ft_appendtimelock
‘yes’, ‘no’, ‘ifmakessense’ (default = ‘ifmakessense’)

** cfg.keeptapers ** - ft_freqanalysis
‘yes’ or ‘no’, return individual tapers or average (default = ‘no’)

** cfg.keeptrial ** - ft_rejectvisual
string, determines how to deal with trials that are not selected, can be ‘no’ completely remove deselected trials from the data (default) ‘yes’ keep deselected trials in the output data ‘nan’ fill the trials that are deselected with NaNs

** cfg.keeptrials ** - ft_mvaranalysis
‘no’ (default) or ‘yes’ specifies whether the coefficients are estimated for each trial seperately, or on the concatenated data

** cfg.keeptrials ** - ft_sourceanalysis
‘no’ or ‘yes’

** cfg.keeptrials ** - ft_sourcedescriptives
‘yes’ or ‘no’ (default = ‘no’)

** cfg.keeptrials ** - ft_spike_jpsth, ft_spike_psth, ft_spike_xcorr
‘yes’ or ‘no’ (default)

** cfg.keeptrials ** - ft_spike_rate
‘yes’ or ‘no’ (default).

** cfg.keeptrials ** - ft_spikedensity
‘yes’ or ‘no’ (default). If ‘yes’, we store the trials in a matrix in the output SDF as well

** cfg.keeptrials ** - ft_freqdescriptives
‘yes’ or ‘no’, estimate single trial power (useful for fourier data) (default = ‘no’)

** cfg.keeptrials ** - ft_nonlinearassociation
‘yes’ or ‘no’, process the individual trials or the concatenated data (default = ‘no’)

** cfg.keeptrials ** - ft_freqanalysis, ft_spiketriggeredaverage, ft_timelockanalysis
‘yes’ or ‘no’, return individual trials or average (default = ‘no’)

** cfg.keeptrials ** - ft_crossfrequencyanalysis
string, can be ‘yes’ or ‘no’

** cfg.keepvalue ** - ft_anonymizedata
cell-array with strings, values to keep (default = {})

** cfg.kmeans ** - ft_spikesorting
substructure with additional low-level options for this method

** cfg.kurtosis ** - ft_sourcedescriptives
‘yes’ or ‘no’ (default = ‘no’)

L

** cfg.lambda ** - ft_omri_quality
forgetting factor for the variaton plot (default=0.9)

** cfg.lambda ** - ft_sourceanalysis
number or empty for automatic default

** cfg.lambda ** - ft_channelrepair
regularisation parameter (default = 1e-5, not for method ‘distance’)

** cfg.lambda ** - ft_scalpcurrentdensity
regularization parameter (default = 1e-05)

** cfg.latency ** - ft_spikedetection, ft_spikedownsample
[b1 e1; b2 e2; …]

** cfg.latency ** - ft_spiketriggeredspectrum_stat
[beg end] in sec, or ‘maxperiod’, ‘poststim’ or ‘prestim’. This determines the start and end of analysis window.

** cfg.latency ** - ft_spike_rate
[begin end] in seconds ‘maxperiod’ (default) ‘minperiod’, i.e., the minimal period all trials share ‘prestim’ (all t<=0) ‘poststim’ (all t>=0).

** cfg.latency ** - ft_spike_select
[begin end] in seconds ‘maxperiod’ (default), i.e., maximum period available ‘minperiod’, i.e., the minimal period all trials share ‘prestim’ (all t<=0) ‘poststim’ (all t>=0).

** cfg.latency ** - ft_spike_psth
[begin end] in seconds ‘maxperiod’ (default), i.e., maximum period available ‘minperiod’, i.e., the minimal period all trials share, ‘prestim’ (all t<=0) ‘poststim’ (all t>=0).

** cfg.latency ** - ft_dipolefitting, ft_freqstatistics, ft_timelockgrandaverage, ft_timelockstatistics
[begin end] in seconds or ‘all’ (default = ‘all’)

** cfg.latency ** - ft_spike_plot_jpsth
[begin end] in seconds or ‘max’ (default), ‘prestim’ or ‘poststim’;

** cfg.latency ** - ft_spike_isi
[begin end] in seconds, ‘max’ (default), ‘min’, ‘prestim’(t<=0), or ‘poststim’ (t>=0). If ‘max’, we use all available latencies. If ‘min’, we use only the time window contained by all trials. If ‘prestim’ or ‘poststim’, we use time to or from 0, respectively.

** cfg.latency ** - ft_spike_xcorr
[begin end] in seconds, ‘max’ (default), ‘min’, ‘prestim’(t<=0), or ‘poststim’ (t>=0).%

** cfg.latency ** - ft_spike_plot_raster
[begin end] in seconds, ‘maxperiod’ (default), ‘minperiod’, ‘prestim’ (all t<=0), or ‘poststim’ (all t>=0). If a third input is present, we will use the timelock.cfg.latency field to ensure that the raster and the timelock data have the same latency.

** cfg.latency ** - ft_spikedensity
[begin end] in seconds, ‘maxperiod’ (default), ‘minperiod’, ‘prestim’(t>=0), or ‘poststim’ (t>=0).

** cfg.latency ** - ft_spike_jpsth
[begin end] in seconds, ‘maxperiod’ (default), ‘prestim’(t<=0), or ‘poststim’ (t>=0)

** cfg.latency ** - ft_spike_plot_psth
[begin end] in seconds, ‘maxperiod’ (default), ‘prestim’(t<=0), or ‘poststim’ (t>=0).

** cfg.latency ** - ft_rejectvisual, ft_timelockanalysis
[begin end] in seconds, or ‘all’, ‘minperiod’, ‘maxperiod’, ‘prestim’, ‘poststim’ (default = ‘all’)

** cfg.latency ** - ft_spikesplitting
[begin end], (default = ‘all’)

** cfg.latency ** - ft_spikedetection, ft_spikedownsample
[begin end], default is [0 inf]

** cfg.latency ** - ft_freqdescriptives
[tmin tmax] or ‘all’, to specify a subset of latencies (default = ‘all’)

** cfg.latency ** - ft_sourceplot
scalar or string, can be ‘all’, ‘prestim’, ‘poststim’, or [beg end], specify time range in seconds

** cfg.latency ** - ft_sourceanalysis
single number in seconds, for time-frequency analysis

** cfg.layout ** - ft_prepare_layout
‘butterfly’ will give you a layout with all channels on top of each other

** cfg.layout ** - ft_prepare_layout
‘circular’ will distribute the channels on a circle

** cfg.layout ** - ft_prepare_layout
‘horizontal’ will give you a 1xN ordered layout

** cfg.layout ** - ft_layoutplot
‘ordered’

** cfg.layout ** - ft_prepare_layout
‘ordered’ will give you a NxN ordered layout

** cfg.layout ** - ft_prepare_layout
‘vertical’ will give you a Nx1 ordered layout

** cfg.layout ** - ft_prepare_layout
filename containg the input layout (*.mat or *.lay file), this can also be a layout structure, which is simply returned as-is (see below for details)

** cfg.layout ** - ft_layoutplot
filename containg the layout

** cfg.layout ** - ft_databrowser, ft_neighbourplot, ft_prepare_neighbours
filename of the layout, see FT_PREPARE_LAYOUT

** cfg.layout ** - ft_topoplotCC
specification of the layout, see FT_PREPARE_LAYOUT

** cfg.layout ** - ft_movieplotER, ft_movieplotTFR, ft_topoplotIC
specification of the layout, see below

** cfg.layout ** - ft_multiplotER, ft_multiplotTFR, ft_topoplotER, ft_topoplotTFR
specify the channel layout for plotting using one of the supported ways (see below).

** cfg.length ** - ft_redefinetrial
single number (in unit of time, typically seconds) of the required snippets

** cfg.level1.condition ** - ft_steadystatesimulation
scalar, or vector of length L1 (default = 1)

** cfg.level1.gain ** - ft_steadystatesimulation
scalar, or vector of length L1 (default = 1)

** cfg.level2.condition ** - ft_steadystatesimulation
scalar, or vector of length L2 (default = 1)

** cfg.level2.gain ** - ft_steadystatesimulation
scalar, or vector of length L2 (default = 1)

** cfg.level3.condition ** - ft_steadystatesimulation
scalar, or vector of length L3 (default = 1)

** cfg.level3.gain ** - ft_steadystatesimulation
scalar, or vector of length L3 (default = 1)

** cfg.limittext ** - ft_multiplotER, ft_multiplotTFR
add user-defined text instead of cfg.comment, (default = cfg.comment)

** cfg.linefreq ** - ft_qualitycheck
scalar, frequency of power line (default = 50)

** cfg.linestyle ** - ft_multiplotER, ft_singleplotER
linestyle/marker type, see options of the PLOT function (default = ‘-‘) can be a single style for all datasets, or a cell-array containing one style for each dataset

** cfg.linewidth ** - ft_multiplotER, ft_singleplotER
linewidth in points (default = 0.5)

** cfg.linewidth ** - ft_spike_plot_raster
number indicating the width of the lines (default = 1);

** cfg.linewidth ** - ft_databrowser
number, width of plotted lines (default = 0.5)

** cfg.location ** - ft_sourceplot
location of cut, (default = ‘auto’) ‘auto’, ‘center’ if only anatomy, ‘max’ if functional data ‘min’ and ‘max’ position of min/max funparameter ‘center’ of the brain [x y z], coordinates in voxels or head, see cfg.locationcoordinates

** cfg.locationcoordinates ** - ft_sourceplot
coordinate system used in cfg.location, ‘head’ or ‘voxel’ (default = ‘head’) ‘head’, headcoordinates as mm or cm ‘voxel’, voxelcoordinates as indices

** cfg.lpfiltdev ** - ft_preprocessing
lowpass max passband deviation (firws with ‘kaiser’ window, default 0.001 set in low-level function)

** cfg.lpfiltdf ** - ft_preprocessing
lowpass transition width (firws, overrides order, default set in low-level function)

** cfg.lpfiltdir ** - ft_preprocessing
filter direction, ‘twopass’ (default), ‘onepass’ or ‘onepass-reverse’ or ‘onepass-zerophase’ (default for firws) or ‘onepass-minphase’ (firws, non-linear!)

** cfg.lpfilter ** - ft_preprocessing
‘no’ or ‘yes’ lowpass filter (default = ‘no’)

** cfg.lpfiltord ** - ft_preprocessing
lowpass filter order (default set in low-level function)

** cfg.lpfilttype ** - ft_preprocessing
digital filter type, ‘but’ or ‘firws’ or ‘fir’ or ‘firls’ (default = ‘but’)

** cfg.lpfiltwintype ** - ft_preprocessing
lowpass window type, ‘hann’ or ‘hamming’ (default) or ‘blackman’ or ‘kaiser’ (firws)

** cfg.lpfreq ** - ft_preprocessing
lowpass frequency in Hz

** cfg.lpinstabilityfix ** - ft_preprocessing
deal with filter instability, ‘no’, ‘reduce’, ‘split’ (default = ‘no’)

M

** cfg.magradius ** - ft_electrodeplacement
number representing the radius for the cfg.magtype based search (default = 3)

** cfg.magscale ** - ft_multiplotER, ft_multiplotTFR
number, scaling to apply to the MEG magnetometer channels prior to display

** cfg.magscale ** - ft_databrowser, ft_rejectvisual
number, scaling to apply to the MEG magnetometer channels prior to display (in addition to the cfg.megscale factor)

** cfg.magtype ** - ft_electrodeplacement
string representing the ‘magnet’ type used for placing the electrodes ‘peakweighted’ place electrodes at weighted peak intensity voxel (default) ‘troughweighted’ place electrodes at weighted trough intensity voxel ‘peak’ place electrodes at peak intensity voxel (default) ‘trough’ place electrodes at trough intensity voxel ‘weighted’ place electrodes at center-of-mass

** cfg.markcorner ** - ft_volumewrite
‘yes’ or ‘no’, mark the first corner of the volume

** cfg.marker ** - ft_topoplotER, ft_topoplotIC, ft_topoplotTFR
‘on’, ‘labels’, ‘numbers’, ‘off’

** cfg.marker ** - ft_sliceinterp
[Nx3] array defining N marker positions to display

** cfg.markercolor ** - ft_sliceinterp
[1x3] marker color in RGB (default = [1 1 1], i.e. white)

** cfg.markercolor ** - ft_topoplotER, ft_topoplotIC, ft_topoplotTFR
channel marker color (default = [0 0 0] (black))

** cfg.markerfontsize ** - ft_topoplotER, ft_topoplotIC, ft_topoplotTFR
font size of channel labels (default = 8 pt)

** cfg.markersize ** - ft_topoplotER, ft_topoplotIC, ft_topoplotTFR
channel marker size (default = 2)

** cfg.markersize ** - ft_sliceinterp
radius of markers (default = 5);

** cfg.markersymbol ** - ft_topoplotER, ft_topoplotIC, ft_topoplotTFR
channel marker symbol (default = ‘o’)

** cfg.markfiducial ** - ft_volumewrite
‘yes’ or ‘no’, mark the fiducials

** cfg.markorigin ** - ft_volumewrite
‘yes’ or ‘no’, mark the origin

** cfg.mask ** - ft_layoutplot
string, ‘yes’ or ‘no’ whether the mask should be plotted (default = ‘yes’)

** cfg.mask ** - ft_prepare_layout
string, how to create the mask, can be ‘circle’, ‘convex’, ‘headshape’, ‘mri’ or ‘no’ (default is automatic)

** cfg.maskclipmax ** - ft_sliceinterp
value or ‘auto’ (clipping of mask data)

** cfg.maskclipmin ** - ft_sliceinterp
value or ‘auto’ (clipping of mask data)

** cfg.maskclipsym ** - ft_sliceinterp
‘yes’ or ‘no’ (default) symmetrical clipping

** cfg.maskcolmin ** - ft_sliceinterp
mask value mapped to the highest opacity, i.e. non-transparent (default = ‘auto’)

** cfg.maskcolmin ** - ft_sliceinterp
mask value mapped to the lowest opacity, i.e. completely transparent (default =’auto’)

** cfg.maskmap ** - ft_sliceinterp
opacitymap for source overlay (default is linspace(0,1,128))

** cfg.masknans ** - ft_multiplotTFR, ft_singleplotTFR
‘yes’ or ‘no’ (default = ‘yes’)

** cfg.maskparameter ** - ft_multiplotTFR, ft_singleplotTFR
field in the data to be used for masking of data, can be logical (e.g. significant data points) or numerical (e.g. t-values). (not possible for mean over multiple channels, or when input contains multiple subjects or trials)

** cfg.maskparameter ** - ft_topoplotER, ft_topoplotTFR
field in the data to be used for masking of data. It should have alues between 0 and 1, where 0 corresponds to transparent.

** cfg.maskparameter ** - ft_multiplotER
field in the first dataset to be used for marking significant data

** cfg.maskparameter ** - ft_singleplotER
field in the first dataset to be used for masking of data (not possible for mean over multiple channels, or when input contains multiple subjects or trials)

** cfg.maskparameter ** - ft_sliceinterp
parameter used as opacity mask (default = ‘none’)

** cfg.maskparameter ** - ft_sourceplot
string, field in the data to be used for opacity masking of fun data (default = []) If values are between 0 and 1, zero is fully transparant and one is fully opaque. If values in the field are not between 0 and 1 they will be scaled depending on the values of cfg.opacitymap and cfg.opacitylim (see below) You can use masking in several ways, f.i. - use outcome of statistics to show only the significant values and mask the insignificant NB see also cfg.opacitymap and cfg.opacitylim below - use the functional data itself as mask, the highest value (and/or lowest when negative) will be opaque and the value closest to zero transparent - Make your own field in the data with values between 0 and 1 to control opacity directly

** cfg.maskparameter ** - ft_volumelookup
string, field in volume to be looked up, data in field should be logical

** cfg.maskparameter ** - ft_sourcemovie
string, functional parameter that is used for opacity (default = [])

** cfg.maskstyle ** - ft_sourceplot
‘opacity’, or ‘colormix’. If ‘opacity’, low-level graphics opacity masking is applied, if ‘colormix’, the color data is explicitly expressed as a single RGB value, incorporating the opacitymask. Yields faster and more robust rendering in general.

** cfg.maskstyle ** - ft_multiplotER, ft_singleplotER
style used for masking of data, ‘box’, ‘thickness’ or ‘saturation’ (default = ‘box’)

** cfg.maskstyle ** - ft_multiplotTFR, ft_singleplotTFR
style used to masking, ‘opacity’, ‘saturation’, or ‘outline’ (default = ‘opacity’) ‘outline’ can only be used with a logical cfg.maskparameter use ‘saturation’ or ‘outline’ when saving to vector-format (like *.eps) to avoid all sorts of image-problems

** cfg.match ** - ft_recodeevent
‘exact’ or ‘nearest’

** cfg.matfile ** - ft_qualitycheck
string, filename (e.g. ‘previousoutput.mat’), preferably in combination with analyze = ‘no’

** cfg.maxAbs ** - ft_omri_quality
threshold (mm) for absolute motion before ‘A’ is sent to serial port, default = Inf

** cfg.maxRel ** - ft_omri_quality
threshold (mm) for relative motion before ‘B’ is sent to serial port, default = Inf

** cfg.maxdelay ** - ft_nonlinearassociation
32/cfg.fsample

** cfg.maxlag ** - ft_spike_xcorr
number in seconds, indicating the maximum lag for the cross-correlation function in sec (default = 0.1 sec).

** cfg.maxqueryrange ** - ft_volumelookup, ft_volumelookup
number, should be odd and >= to minqueryrange (default = 1)

** cfg.maxradius ** - ft_prepare_headmodel
(optional)

** cfg.medianfilter ** - ft_preprocessing
‘no’ or ‘yes’ jump preserving median filter (default = ‘no’)

** cfg.medianfiltord ** - ft_preprocessing
length of median filter (default = 9)

** cfg.medianwindow ** - ft_electrodermalactivity
scalar, length of window for median filter in seconds (default = 8)

** cfg.megscale ** - ft_databrowser, ft_rejectvisual
number, scaling to apply to the MEG channels prior to display

** cfg.memory ** - ft_artifact_zvalue
‘low’ or ‘high’, whether to be memory or computationally efficient, respectively (default = ‘high’)

** cfg.method ** - ft_timelockgrandaverage
‘across’ (default) or ‘within’, see below.

** cfg.method ** - ft_defacevolume
‘box’, ‘spm’ (default = ‘box’)

** cfg.method ** - ft_prepare_mesh
‘cortexhull’;

** cfg.method ** - ft_artifact_tms
‘detect’ or ‘marker’, see below. markers written in the EEG.

** cfg.method ** - ft_prepare_neighbours
‘distance’, ‘triangulation’ or ‘template’

** cfg.method ** - ft_scalpcurrentdensity
‘finite’ for finite-difference method or ‘spline’ for spherical spline method ‘hjorth’ for Hjorth approximation method

** cfg.method ** - ft_electroderealign, ft_electroderealign
‘headshape’

** cfg.method ** - ft_stratify
‘histogram’ ‘splithilo’ ‘splitlohi’ ‘splitlolo’ ‘splithihi’ ‘equatespike’

** cfg.method ** - ft_spike_jpsth
‘jpsth’ or ‘shiftpredictor’. If ‘jpsth’, we output the normal stat. If ‘shiftpredictor’, we compute the jpsth after shuffling subsequent trials.

** cfg.method ** - ft_spikesorting
‘kmeans’, ‘ward’

** cfg.method ** - ft_sourceanalysis
‘lcmv’ linear constrained minimum variance beamformer ‘sam’ synthetic aperture magnetometry ‘dics’ dynamic imaging of coherent sources ‘pcc’ partial cannonical correlation/coherence ‘mne’ minimum norm estimation ‘rv’ scan residual variance with single dipole ‘music’ multiple signal classification ‘sloreta’ standardized low-resolution electromagnetic tomography ‘eloreta’ exact low-resolution electromagnetic tomography

** cfg.method ** - ft_spiketriggeredspectrum
‘mtmfft’ or ‘mtmconvol’ (see below)

** cfg.method ** - ft_freqinterpolate
‘nan’, ‘linear’ (default = ‘nan’)

** cfg.method ** - ft_channelnormalise
‘perchannel’, or ‘acrosschannel’, computes the standard deviation per channel, or across all channels. The latter method leads to the same scaling across channels and preserves topographical distributions

** cfg.method ** - ft_componentanalysis
‘runica’, ‘fastica’, ‘binica’, ‘pca’, ‘svd’, ‘jader’, ‘varimax’, ‘dss’, ‘cca’, ‘sobi’, ‘white’ or ‘csp’ (default = ‘runica’)

** cfg.method ** - ft_sourceplot
‘slice’, plots the data on a number of slices in the same plane ‘ortho’, plots the data on three orthogonal slices ‘surface’, plots the data on a 3D brain surface ‘glassbrain’, plots a max-projection through the brain ‘vertex’, plots the grid points or vertices scaled according to the functional value ‘cloud’, plot the data as clouds, spheres, or points scaled according to the functional value

** cfg.method ** - ft_statistics_stats
‘stats’

** cfg.method ** - ft_combineplanar
‘sum’, ‘svd’, ‘abssvd’, or ‘complex’ (default = ‘sum’)

** cfg.method ** - ft_preprocessing
‘trial’ or ‘channel’, read data per trial or per channel (default = ‘trial’)

** cfg.method ** - ft_headmovement
‘updatesens’ (default), ‘cluster’, ‘avgoverrpt’, ‘pertrial_cluster’, ‘pertrial’

** cfg.method ** - ft_channelrepair
‘weighted’, ‘average’, ‘spline’, ‘slap’ or ‘nan’ (default = ‘weighted’)

** cfg.method ** - ft_spike_xcorr
‘xcorr’ or ‘shiftpredictor’. If ‘shiftpredictor’ we do not compute the normal cross-correlation but shuffle the subsequent trials. If two channels are independent, then the shift predictor should give the same correlogram as the raw correlogram calculated from the same trials. Typically, the shift predictor is subtracted from the correlogram.

** cfg.method ** - ft_freqsimulation
The methods are explained in more detail below, but they can be ‘superimposed’ simply add the contribution of the different frequencies ‘broadband’ create a single broadband signal component ‘phalow_amphigh’ phase of low freq correlated with amplitude of high freq ‘amplow_amphigh’ amplitude of low freq correlated with amplithude of high freq ‘phalow_freqhigh’ phase of low freq correlated with frequency of high signal ‘asymmetric’ single signal component with asymmetric positive/negative deflections

** cfg.method ** - ft_sourcestatistics
different methods for calculating the probability of the null-hypothesis, ‘montecarlo’ uses a non-parametric randomization test to get a Monte-Carlo estimate of the probability, ‘analytic’ uses a parametric test that results in analytic probability, ‘stats’ (soon deprecated) uses a parametric test from the MATLAB statistics toolbox,

** cfg.method ** - ft_freqstatistics, ft_timelockstatistics
different methods for calculating the significance probability and/or critical value ‘montecarlo’ get Monte-Carlo estimates of the significance probabilities and/or critical values from the permutation distribution, ‘analytic’ get significance probabilities and/or critical values from the analytic reference distribution (typically, the sampling distribution under the null hypothesis), ‘stats’ use a parametric test from the MATLAB statistics toolbox, ‘crossvalidate’ use crossvalidation to compute predictive performance

** cfg.method ** - ft_freqanalysis
different methods of calculating the spectra ‘mtmfft’, analyses an entire spectrum for the entire data length, implements multitaper frequency transformation ‘mtmconvol’, implements multitaper time-frequency transformation based on multiplication in the frequency domain. ‘wavelet’, implements wavelet time frequency transformation (using Morlet wavelets) based on multiplication in the frequency domain. ‘tfr’, implements wavelet time frequency transformation (using Morlet wavelets) based on convolution in the time domain. ‘mvar’, does a fourier transform on the coefficients of an estimated multivariate autoregressive model, obtained with FT_MVARANALYSIS. In this case, the output will contain a spectral transfer matrix, the cross-spectral density matrix, and the covariance matrix of the innovatio noise.

** cfg.method ** - ft_detect_movement
different methods of detecting different movement types ‘velocity2D’, Micro/saccade detection based on Engbert R, Kliegl R (2003) Vision Res 43:1035-1045. The method computes thresholds based on velocity changes from eyetracker data (horizontal and vertical components). ‘clustering’, Micro/saccade detection based on Otero-Millan et al., (2014) J Vis 14 (not implemented yet)

** cfg.method ** - ft_resampledata
interpolation method, see INTERP1 (default = ‘pchip’)

** cfg.method ** - ft_spike_rate_orituning
model to apply, implemented are ‘orientation’ and ‘direction’

** cfg.method ** - ft_spikedownsample
resampling method, can be ‘resample’, ‘decimate’ or ‘downsample’

** cfg.method ** - ft_volumerealign
string representing the method for aligning ‘interactive’ use the GUI to specify the fiducials ‘fiducial’ use pre-specified fiducials ‘headshape’ match the MRI surface to a headshape ‘spm’ match to template anatomical MRI ‘fsl’ match to template anatomical MRI

** cfg.method ** - ft_electroderealign
string representing the method for aligning or placing the electrodes ‘interactive’ realign manually using a graphical user interface ‘fiducial’ realign using three fiducials (e.g. NAS, LPA and RPA) ‘template’ realign the electrodes to match a template set ‘headshape’ realign the electrodes to fit the head surface ‘project’ projects electrodes onto the head surface ‘moveinward’ moves electrodes inward along their normals

** cfg.method ** - ft_electrodeplacement
string representing the method for placing the electrodes ‘volume’ interactively locate electrodes on three orthogonal slices of a volumetric MRI or CT scan ‘headshape’ interactively locate electrodes on a head surface ‘1020’ automatically locate electrodes on a head surface according to the 10-20 system ‘shaft’ automatically locate electrodes along a linear sEEG shaft ‘grid’ automatically locate electrodes on a MxN ECoG grid

** cfg.method ** - ft_prepare_headmodel
string that specifies the forward solution, see below

** cfg.method ** - ft_spikedetection
string with the method to use, can be ‘all’, ‘zthresh’, ‘ztrig’, ‘flank’

** cfg.method ** - ft_volumereslice
string, ‘flip’, ‘nearest’, ‘linear’, ‘cubic’ or ‘spline’ (default = ‘linear’)

** cfg.method ** - ft_denoise_tsr
string, ‘mlr’, ‘cca’, ‘pls’, ‘svd’, option specifying the criterion for the regression (default = ‘mlr’)

** cfg.method ** - ft_spiketriggeredinterpolation
string, The interpolation method can be ‘nan’, ‘cubic’, ‘linear’, ‘nearest’, spline’, ‘pchip’ (default = ‘nan’). See INTERP1 for more details.

** cfg.method ** - ft_connectivityanalysis
string, can be ‘amplcorr’, amplitude correlation, support for freq and source data ‘coh’, coherence, support for freq, freqmvar and source data. For partial coherence also specify cfg.partchannel, see below. For imaginary part of coherency or coherency also specify cfg.complex, see below. ‘csd’, cross-spectral density matrix, can also calculate partial csds - if cfg.partchannel is specified, support for freq and freqmvar data ‘dtf’, directed transfer function, support for freq and freqmvar data ‘granger’, granger causality, support for freq and freqmvar data ‘pdc’, partial directed coherence, support for freq and freqmvar data ‘plv’, phase-locking value, support for freq and freqmvar data ‘powcorr’, power correlation, support for freq and source data ‘powcorr_ortho’, power correlation with single trial orthogonalisation, support for source data ‘ppc’ pairwise phase consistency ‘psi’, phaseslope index, support for freq and freqmvar data ‘wpli’, weighted phase lag index (signed one, still have to take absolute value to get indication of strength of interaction. Note: measure has positive bias. Use wpli_debiased to avoid this. ‘wpli_debiased’ debiased weighted phase lag index (estimates squared wpli) ‘wppc’ weighted pairwise phase consistency ‘corr’ Pearson correlation, support for timelock or raw data

** cfg.method ** - ft_crossfrequencyanalysis
string, can be ‘coh’ - coherence ‘plv’ - phase locking value ‘mvl’ - mean vector length ‘mi’ - modulation index

** cfg.method ** - ft_meshrealign
string, can be ‘interactive’ or fiducial’ (default = ‘interactive’)

** cfg.method ** - ft_prepare_mesh
string, can be ‘interactive’, ‘projectmesh’, ‘iso2mesh’, ‘isosurface’, ‘headshape’, ‘hexahedral’, ‘tetrahedral’, ‘cortexhull’

** cfg.method ** - ft_connectivitysimulation
string, can be ‘linear_mix’, ‘mvnrnd’, ‘ar’, ‘ar_reverse’ (see below)

** cfg.method ** - ft_rejectvisual
string, describes how the data should be shown, this can be ‘summary’ show a single number for each channel and trial (default) ‘channel’ show the data per channel, all trials at once ‘trial’ show the data per trial, all channels at once

** cfg.method ** - ft_globalmeanfield
string, determines whether the amplitude or power should be calculated (see below, default is ‘amplitude’, can be ‘power’)

** cfg.method ** - ft_interpolatenan
string, interpolation method, see HELP INTERP1 (default = ‘linear’)

** cfg.method ** - ft_sourceparcellate
string, method to combine the values, see below (default = ‘mean’)

** cfg.method ** - ft_networkanalysis
string, specifying the graph measure that will be computed. See below for the list of supported measures.

** cfg.method ** - ft_mvaranalysis
the name of the toolbox containing the function for the actual computation of the ar-coefficients this can be ‘biosig’ (default) or ‘bsmart’ you should have a copy of the specified toolbox in order to use mvaranalysis (both can be downloaded directly).

** cfg.metric ** - ft_rejectvisual
string, describes the metric that should be computed in summary mode for each channel in each trial, can be ‘var’ variance within each channel (default) ‘min’ minimum value in each channel ‘max’ maximum value each channel ‘maxabs’ maximum absolute value in each channel ‘range’ range from min to max in each channel ‘kurtosis’ kurtosis, i.e. measure of peakedness of the amplitude distribution ‘zvalue’ mean and std computed over all time and trials, per channel

** cfg.minlength ** - ft_redefinetrial
length in seconds, can be ‘maxperlen’ (default = [])

** cfg.minqueryrange ** - ft_volumelookup, ft_volumelookup
number, should be odd and <= to maxqueryrange (default = 1)

** cfg.minspace ** - ft_sourceplot
scalar, minimum spacing between slices if nslices>1 (default = 1)

** cfg.missingchannel ** - ft_channelrepair
cell-array, see FT_CHANNELSELECTION for details

** cfg.mix ** - ft_connectivitysimulation
matrix, [nsignal x number of unobserved signals] specifying the mixing from the unobserved signals to the observed signals, or = matrix, [nsignal x number of unobserved signals x number of samples] specifying the mixing from the unobserved signals to the observed signals which changes as a function of time within the trial = cell-arry, [1 x ntrials] with each cell a matrix as specified above, when a trial-specific mixing is required

** cfg.model ** - ft_dipolefitting
‘moving’ or ‘regional’

** cfg.montage ** - ft_layoutplot, ft_prepare_layout
‘no’ or a montage structure (default = ‘no’)

** cfg.montage ** - ft_preprocessing
‘no’ or a montage structure, see FT_APPLY_MONTAGE (default = ‘no’)

** cfg.moveinward ** - ft_prepare_sourcemodel
number, move dipoles inward to ensure a certain distance to the innermost surface of the source compartment (default = 0)

** cfg.moveinward ** - ft_electroderealign
number, the distance that the electrode should be moved inward (negative numbers result in an outward move)

** cfg.moviefreq ** - ft_movieplotTFR
number, movie frames are all time points at the fixed frequency moviefreq (default = []);

** cfg.movietime ** - ft_movieplotTFR
number, movie frames are all frequencies at the fixed time movietime (default = []);

** cfg.mri ** - ft_prepare_sourcemodel
can be filename or MRI structure, containing the individual anatomy

** cfg.mri ** - ft_prepare_sourcemodel
can be filename, MRI structure or segmented MRI structure

** cfg.mri ** - ft_prepare_layout
segmented anatomical MRI to be used for generating an outline, see FT_READ_MRI and FT_VOLUMESEGMENT for details

** cfg.mva ** - ft_statistics_crossvalidate
a multivariate analysis (default = {dml.standardizer dml.svm})

** cfg.mvarmethod ** - ft_mvaranalysis
scalar (only required when cfg.method = ‘biosig’). default is 2, relates to the algorithm used for the computation of the AR-coefficients by mvar.m

** cfg.mychan ** - ft_databrowser
Nx1 cell-array with selection of channels

** cfg.mychanscale ** - ft_databrowser
number, scaling to apply to the channels specified in cfg.mychan

N

** cfg.n1.ampl ** - ft_freqsimulation
root-mean-square amplitude of wide-band signal prior to filtering

** cfg.n1.bpfreq ** - ft_freqsimulation
[Flow Fhigh]

** cfg.n2.ampl ** - ft_freqsimulation
root-mean-square amplitude of wide-band signal prior to filtering

** cfg.n2.bpfreq ** - ft_freqsimulation
[Flow Fhigh]

** cfg.name ** - ft_volumenormalise, ft_volumesegment
string for output filename

** cfg.nearestto ** - ft_recodeevent
‘trialzero’ compare with time t=0 for each trial (default) ‘trialbegin’ compare with the begin of each trial ‘trialend’ compare with the end of each trial

** cfg.neighbourdist ** - ft_prepare_neighbours
number, maximum distance between neighbouring sensors (only for ‘distance’)

** cfg.neighbours ** - ft_freqstatistics, ft_megplanar, ft_scalpcurrentdensity, ft_statistics_montecarlo
neighbourhood structure, see FT_PREPARE_NEIGHBOURS

** cfg.neighbours ** - ft_neighbourplot
neighbourhood structure, see FT_PREPARE_NEIGHBOURS (optional)

** cfg.neighbours ** - ft_channelrepair
neighbourhood structure, see also FT_PREPARE_NEIGHBOURS

** cfg.neighbours ** - ft_rejectvisual
neighbourhood structure, see also FT_PREPARE_NEIGHBOURS (required for repairing channels)

** cfg.nfold ** - ft_denoise_tsr
scalar, indicating the number of test folds to use in a cross-validation scheme

** cfg.nfolds ** - ft_statistics_crossvalidate
number of cross-validation folds (default = 5)

** cfg.noise.ampl ** - ft_freqsimulation
amplitude of noise

** cfg.noise.ampl ** - ft_timelocksimulation
number (default = 0.1)

** cfg.noisecov ** - ft_connectivitysimulation
matrix, [nsignal x nsignal] specifying the covariance matrix of the innovation process

** cfg.nonlinear ** - ft_volumenormalise
‘yes’ (default) or ‘no’, estimates a nonlinear transformation in addition to the linear affine registration. If a reasonably accurate normalisation is sufficient, a purely linearly transformed image allows for ‘reverse-normalisation’, which might come in handy when for example a region of interest is defined on the normalised group-average.

** cfg.nonlinear ** - ft_dipolefitting
‘yes’ or ‘no’, perform nonlinear search for optimal dipole parameters (default = ‘yes’)

** cfg.normalization ** - ft_spike_jpsth
‘no’ (default), or ‘yes’. If requested, the joint psth is normalized as in van Aertsen et al. (1989).

** cfg.normalize ** - ft_sourceanalysis
‘no’ or ‘yes’ (default = ‘no’)

** cfg.normalize ** - ft_spike_waveform
‘yes’ (default) or ‘no’: normalizes all waveforms to have peak-to-through amp of 2

** cfg.normalize ** - ft_prepare_leadfield
‘yes’ or ‘no’ (default = ‘no’)

** cfg.normalize ** - ft_regressconfound
string, ‘yes’ or ‘no’, normalization to make the confounds orthogonal (default = ‘yes’)

** cfg.normalizeparam ** - ft_prepare_leadfield
depth normalization parameter (default = 0.5)

** cfg.normalizevar ** - ft_timelockgrandaverage
‘N’ or ‘N-1’ (default = ‘N-1’)

** cfg.nr_bins ** - ft_nonlinearassociation
7

** cfg.nsignal ** - ft_connectivitysimulation
scalar, number of signals

** cfg.nslices ** - ft_sliceinterp
integer value, default is 20

** cfg.nslices ** - ft_sourceplot
number of slices, (default = 20)

** cfg.nslices ** - ft_sourceplot
scalar, number of slices to plot if ‘slicepos’ = ‘auto (default = 1)

** cfg.ntrials ** - ft_steadystatesimulation
integer N, number of trials (default = 320)

** cfg.ntrials ** - ft_dipolesimulation
number of trials

** cfg.ntrials ** - ft_connectivitysimulation
scalar, number of trials

** cfg.numDummy ** - ft_omri_pipeline
how many scans to ignore initially (default 0)

** cfg.numDummy ** - ft_omri_pipeline_nuisance
how many scans to ignore initially (default 4)

** cfg.numDummy ** - ft_omri_quality
how many scans to ignore initially (default=0)

** cfg.numRegr ** - ft_omri_pipeline_nuisance
number of nuisance regressors (1=constant term, 2=const+linear,5=const,linear+translation)

** cfg.numbin ** - ft_stratify
10

** cfg.numbootstrap ** - ft_sourceanalysis
number of bootstrap replications (e.g. number of original trials)

** cfg.numchans ** - ft_spikefixdmafile
number of channels (default = 256)

** cfg.numclusters ** - ft_headmovement
number of segments with constant headposition in which to split the data (default = 10). This argument is used in some of the methods only (see below), and is used in a kmeans clustering scheme.

** cfg.numcomponent ** - ft_componentanalysis
‘all’ or number (default = ‘all’)

** cfg.numdipoles ** - ft_dipolefitting
number, default is 1

** cfg.numiter ** - ft_stratify
2000

** cfg.numpermutation ** - ft_sourceanalysis
number, e.g. 500 or ‘all’

** cfg.numrandomization ** - ft_statistics_montecarlo
number of randomizations, can be ‘all’

** cfg.numrandomization ** - ft_sourceanalysis
number, e.g. 500

** cfg.numtrl ** - ft_freqsimulation
number of simulated trials

** cfg.numtrl ** - ft_timelocksimulation
number of simulated trials (default = 10)

** cfg.numvertices ** - ft_prepare_mesh
[800, 1600, 2400]; bnd = ft_prepare_mesh(cfg, segmentation);

** cfg.numvertices ** - ft_prepare_mesh
numeric vector, should have same number of elements as cfg.tissue

O

** cfg.offset ** - ft_nonlinearassociation
0

** cfg.offset ** - ft_redefinetrial
single number or Nx1 vector, expressed in samples relative to current t=0

** cfg.opacitylim ** - ft_sourceplot
range of mask values to which opacitymap is scaled (default = ‘auto’) [min max] ‘maxabs’, from -max(abs(maskparameter)) to +max(abs(maskparameter)) ‘zeromax’, from 0 to max(abs(maskparameter)) ‘minzero’, from min(abs(maskparameter)) to 0 ‘auto’, if maskparameter values are all positive: ‘zeromax’, all negative: ‘minzero’, both positive and negative: ‘maxabs’

** cfg.opacitymap ** - ft_sourceplot
opacitymap for mask data, see ALPHAMAP (default = ‘auto’) ‘auto’, depends structure maskparameter, or on opacitylim - maskparameter: only positive values, or opacitylim:’zeromax’ -> ‘rampup’ - maskparameter: only negative values, or opacitylim:’minzero’ -> ‘rampdown’ - maskparameter: both pos and neg values, or opacitylim:’maxabs’ -> ‘vdown’ - opacitylim: [min max] if min & max pos-> ‘rampup’, neg-> ‘rampdown’, both-> ‘vdown’ - NB. to use p-values use ‘rampdown’ to get lowest p-values opaque and highest transparent

** cfg.openmeeg.batchsize ** - ft_prepare_leadfield
scalar (default 100e3), number of dipoles for which the leadfield is computed in a single call to the low-level code. Trades off memory efficiency for speed.

** cfg.openmeeg.dsm ** - ft_prepare_leadfield
‘no’/’yes’, reuse existing DSM if provided

** cfg.openmeeg.keepdsm ** - ft_prepare_leadfield
‘no’/’yes’, option to retain DSM (no by default)

** cfg.openmeeg.nonadaptive ** - ft_prepare_leadfield
‘no’/’yes’

** cfg.operation ** - ft_math
string, can be ‘add’, ‘subtract’, ‘divide’, ‘multiply’, ‘log10’, ‘abs’

** cfg.operation ** - ft_math
string, for example ‘(x1-x2)/(x1+x2)’ or ‘x1/6’

** cfg.option1 ** - ft_examplefunction
value, explain the value here (default = something)

** cfg.option2 ** - ft_examplefunction
value, describe the value here and if needed continue here to allow automatic parsing of the help

** cfg.option3 ** - ft_examplefunction
value, explain it here (default is automatic)

** cfg.opto ** - ft_channelrepair
structure with optode definition, see FT_DATATYPE_SENS

** cfg.opto ** - ft_prepare_layout
structure with optode structure definition, or

** cfg.optofile ** - ft_prepare_layout
filename containing optode structure definition

** cfg.optofile ** - ft_channelrepair
name of file containing the optode definition, see FT_READ_SENS

** cfg.opts ** - ft_volumesegment
struct, containing spm-version specific options. See the code and/or the SPM-documentation for more detail.

** cfg.opts ** - ft_volumebiascorrect
struct, containing spmversion specific options. See the code below and the SPM-documentation for more information.

** cfg.order ** - ft_nonlinearassociation
‘Hxy’

** cfg.order ** - ft_prepare_headmodel, ft_prepare_headmodel
(optional)

** cfg.order ** - ft_channelrepair
order of the polynomial interpolation (default = 4, not for method ‘distance’)

** cfg.order ** - ft_scalpcurrentdensity
order of the splines (default = 4)

** cfg.order ** - ft_mvaranalysis
scalar, order of the autoregressive model (default=10)

** cfg.ori ** - ft_sourceplot
‘x’, ‘y’, or ‘z’, specifies the orthogonal plane which will be plotted (default = ‘y’)

** cfg.outline ** - ft_prepare_layout
string, how to create the outline, can be ‘circle’, ‘convex’, ‘headshape’, ‘mri’ or ‘no’ (default is automatic)

** cfg.output ** - ft_recodeevent
‘event’ the event itself ‘eventvalue’ the value of the event ‘eventnumber’ the number of the event ‘samplenumber’ the sample at which the event is located ‘samplefromoffset’ number of samples from t=0 (c.f. response time) ‘samplefrombegin’ number of samples from the begin of the trial ‘samplefromend’ number of samples from the end of the trial

** cfg.output ** - ft_freqanalysis
‘pow’ return the power-spectra ‘powandcsd’ return the power and the cross-spectra ‘fourier’ return the complex Fourier-spectra

** cfg.output ** - ft_regressconfound
‘residual’ (default), ‘beta’, or ‘model’. If ‘residual’ is specified, the output is a data structure containing the residuals after regressing out the in cfg.reject listed confounds. If ‘beta’ or ‘model’ is specified, the output is a data structure containing the regression weights or the model, respectively.

** cfg.output ** - ft_volumelookup
‘single’ always outputs one label; if several POI are provided, they are considered together as describing a ROI (default) ‘multiple’ outputs one label per POI (e.g., choose to get labels for different electrodes)

** cfg.output ** - ft_volumesegment
‘skullstrip’; segmented = ft_volumesegment(cfg, mri) will generate a skull-stripped anatomy based on a brainmask generated from the probabilistic tissue maps. The skull-stripped anatomy is stored in the field segmented.anatomy.

** cfg.output ** - ft_prepare_layout
filename (ending in .mat or .lay) to which the layout will be written (default = [])

** cfg.output ** - ft_layoutplot
filename to which the layout will be written (default = [])

** cfg.output ** - ft_volumesegment
string or cell-array of strings, see below (default = ‘tpm’)

** cfg.output ** - ft_spikefixdmafile
string with the name of the DMA log file, (default is determined automatic)

** cfg.output ** - ft_spikesplitting
string with the name of the splitted DMA dataset directory, (default is determined automatic)

** cfg.output ** - ft_spikedetection, ft_spikedownsample
string with the output dataset (default is determined automatic)

** cfg.output ** - ft_omri_pipeline, ft_omri_pipeline_nuisance
where to write processed scans to (default ‘buffer://localhost:1973’)

** cfg.output ** - ft_freqsimulation
which channels should be in the output data, can be ‘mixed’ or ‘all’ (default = ‘all’)

** cfg.output ** - ft_volumesegment
{‘brain’ ‘scalp’ ‘skull’}; segmented = ft_volumesegment(cfg, mri) will produce a volume with 3 binary masks, representing the brain surface, scalp surface, and skull which do not overlap.

** cfg.output ** - ft_volumesegment
{‘brain’}; segment_brain = ft_volumesegment(cfg, segment_tpm);

** cfg.output ** - ft_prepare_mesh
{‘scalp’, ‘skull’, ‘brain’}; segmentation = ft_volumesegment(cfg, mri);

** cfg.output ** - ft_volumesegment
{‘scalp’}; segmented = ft_volumesegment(cfg, mri) will produce a volume with a binary mask (based on the anatomy), representing the border of the scalp surface (i.e., everything inside the surface is also included). Such representation of the scalp is produced faster, because it doesn’t require to create the tissue probabilty maps before creating the mask.

** cfg.output ** - ft_volumesegment
{‘tpm’}; segment_tpm = ft_volumesegment(cfg, mri);

** cfg.outputfile ** - ft_prepare_headmodel, ft_prepare_headmodel
(required) string, filename prefix for the output files

** cfg.outputfile ** - ft_annotate, ft_anonymizedata, ft_appenddata, ft_appendfreq, ft_channelnormalise, ft_channelrepair, ft_combineplanar, ft_componentanalysis, ft_connectivityanalysis, ft_denoise_synthetic, ft_detect_movement, ft_dipolefitting, ft_examplefunction, ft_freqanalysis, ft_freqanalysis_mvar, ft_freqdescriptives, ft_freqgrandaverage, ft_freqinterpolate, ft_freqstatistics, ft_globalmeanfield, ft_interpolatenan, ft_lateralizedpotential, ft_math, ft_megplanar, ft_megrealign, ft_meshrealign, ft_mvaranalysis, ft_prepare_mesh, ft_preprocessing, ft_redefinetrial, ft_regressconfound, ft_rejectcomponent, ft_rejectvisual, ft_removetemplateartifact, ft_resampledata, ft_scalpcurrentdensity, ft_sourceanalysis, ft_sourcedescriptives, ft_sourcegrandaverage, ft_sourceinterpolate, ft_timelockanalysis, ft_timelockbaseline, ft_timelockgrandaverage, ft_timelockstatistics, ft_volumedownsample, ft_volumenormalise, ft_volumerealign, ft_volumereslice, ft_volumesegment

** cfg.outputunit ** - ft_spike_psth
‘rate’ (default) or ‘spikecount’ or ‘proportion’. If ‘rate’, we convert the output per trial to firing rates (spikes/sec). If ‘spikecount’, we count the number spikes per trial. If ‘proportion’, we normalize the area under the PSTH to 1.

** cfg.outputunit ** - ft_spike_rate
‘rate’ (default) or ‘spikecount’. If ‘rate’, we convert the output per trial to firing rates (spikes/sec). If ‘spikecount’, we count the number spikes per trial.

** cfg.outputunit ** - ft_spikedensity
‘rate’ (default) or ‘spikecount’. This determines the physical unit of our spikedensityfunction, either in firing rate or in spikecount.

** cfg.outputunit ** - ft_spike_isi
‘spikecount’ (default) or ‘proportion’ (sum of all bins = 1).

** cfg.outputunit ** - ft_spike_xcorr

  • ‘proportion’ (value in each bin indicates proportion of occurence) - ‘center’ (values are scaled to center value which is set to 1) - ‘raw’ (default) unnormalized crosscorrelogram.

** cfg.overlap ** - ft_redefinetrial
single number (between 0 and 1 (exclusive)) specifying the fraction of overlap between snippets (0 = no overlap)

** cfg.overlap ** - ft_prepare_layout
string, how to deal with overlapping channels when the layout is constructed from a sensor configuration structure. This can be ‘shift’ - shift the positions in 2D space to remove the overlap (default) ‘keep’ - do not shift, retain the overlap ‘no’ - throw an error when overlap is present

P

** cfg.pad ** - ft_freqanalysis
number, ‘nextpow2’, or ‘maxperlen’ (default), length in seconds to which the data can be padded out. The padding will determine your spectral resolution. If you want to compare spectra from data pieces of different lengths, you should use the same cfg.pad for both, in order to spectrally interpolate them to the same spectral resolution. The new option ‘nextpow2’ rounds the maximum trial length up to the next power of 2. By using that amount of padding, the FFT can be computed more efficiently in case ‘maxperlen’ has a large prime factor sum.

** cfg.padding ** - ft_preprocessing
length (in seconds) to which the trials are padded for filtering (default = 0)

** cfg.padtype ** - ft_freqanalysis
string, type of padding (default ‘zero’, see ft_preproc_padding)

** cfg.padtype ** - ft_preprocessing
string, type of padding (default: ‘data’ padding or ‘mirror’, depending on feasibility)

** cfg.pairtrials ** - ft_stratify
‘spikesort’, ‘linkage’ or ‘no’ (default = ‘spikesort’)

** cfg.param ** - ft_spike_isi
string, one of ‘gamfit’ : returns [shape scale] for gamma distribution fit ‘coeffvar’ : coefficient of variation (sd / mean) ‘lv’ : Shinomoto’s Local Variation measure (2009)

** cfg.parameter ** - ft_volumerealign
‘anatomy’ the parameter which is used for the visualization

** cfg.parameter ** - ft_sourceparcellate
cell-array with strings, fields that should be parcellated (default = ‘all’)

** cfg.parameter ** - ft_volumenormalise
cell-array with the functional data to be normalised (default = ‘all’)

** cfg.parameter ** - ft_timelockbaseline
field for which to apply baseline normalization, or cell array of strings to specify multiple fields to normalize (default = ‘avg’)

** cfg.parameter ** - ft_freqbaseline
field for which to apply baseline normalization, or cell array of strings to specify multiple fields to normalize (default = ‘powspctrm’)

** cfg.parameter ** - ft_topoplotER, ft_topoplotTFR
field that contains the data to be plotted as color, for example ‘avg’, ‘powspctrm’ or ‘cohspctrm’ (default is automatic)

** cfg.parameter ** - ft_singleplotER
field to be plotted on y-axis (default depends on data.dimord) ‘avg’, ‘powspctrm’ or ‘cohspctrm’

** cfg.parameter ** - ft_multiplotER
field to be plotted on y-axis, for example ‘avg’, ‘powspctrm’ or ‘cohspctrm’ (default is automatic)

** cfg.parameter ** - ft_singleplotTFR
field to be plotted on z-axis, e.g. ‘powspcrtrm’ (default depends on data.dimord)

** cfg.parameter ** - ft_multiplotTFR
field to be represented as color (default depends on data.dimord) ‘powspctrm’ or ‘cohspctrm’

** cfg.parameter ** - ft_freqstatistics
string (default = ‘powspctrm’)

** cfg.parameter ** - ft_timelockstatistics
string (default = ‘trial’ or ‘avg’)

** cfg.parameter ** - ft_sourceinterpolate
string (or cell-array) of the parameter(s) to be interpolated

** cfg.parameter ** - ft_timelockgrandaverage
string or cell-array indicating which parameter to average. default is set to ‘avg’, if it is present in the data.

** cfg.parameter ** - ft_freqgrandaverage
string or cell-array of strings indicating which parameter(s) to average. default is set to ‘powspctrm’, if it is present in the data.

** cfg.parameter ** - ft_networkanalysis
string specifying the bivariate parameter in the data for which the graph measure will be computed.

** cfg.parameter ** - ft_volumedownsample
string, data field to downsample (default = ‘all’)

** cfg.parameter ** - ft_volumewrite
string, describing the functional data to be processed, e.g. ‘pow’, ‘coh’, ‘nai’ or ‘anatomy’

** cfg.parameter ** - ft_sourcegrandaverage, ft_sourcestatistics
string, describing the functional data to be processed, e.g. ‘pow’, ‘nai’ or ‘coh’

** cfg.parameter ** - ft_math
string, field from the input data on which the operation is performed, e.g. ‘pow’ or ‘avg’

** cfg.parameter ** - ft_electrodeplacement
string, field in data (default = ‘anatomy’ if present in data)

** cfg.parameter ** - ft_sourcewrite
string, functional parameter to be written to file

** cfg.parameter ** - ft_movieplotER, ft_movieplotTFR
string, parameter that is color coded (default = ‘avg’)

** cfg.parameter ** - ft_connectivityplot
string, the functional parameter to be plotted (default = ‘cohspctrm’)

** cfg.parameter ** - ft_appendfreq
string, the name of the field to concatenate

** cfg.params ** - ft_connectivitysimulation
matrix, [nsignal x nsignal x number of lags] specifying the autoregressive coefficient parameters. A non-zero element at cfg.params(i,j,k) means a directional influence from signal j onto signal i (at lag k).

** cfg.parcellation ** - ft_sourceparcellate
string, fieldname that contains the desired parcellation

** cfg.partchannel ** - ft_connectivityanalysis
cell-array containing a list of channels that need to be partialized out, support for method ‘coh’, ‘csd’, ‘plv’

** cfg.peakseparation ** - ft_heartrate, ft_respiration
scalar, time in seconds

** cfg.perchannel ** - ft_denoise_tsr
string, ‘yes’ or ‘no’, or logical, whether or not to perform estimation of beta weights separately per channel

** cfg.permutation ** - ft_sourceanalysis
‘no’ or ‘yes’

** cfg.pertrial ** - ft_denoise_pca
‘no’ (default) or ‘yes’. Regress out the references on a per trial basis

** cfg.planarmethod ** - ft_megplanar
string, can be ‘sincos’, ‘orig’, ‘fitplane’, ‘sourceproject’ (default = ‘sincos’)

** cfg.ploteventlabels ** - ft_databrowser
‘type=value’, ‘colorvalue’ (default = ‘type=value’);

** cfg.plotevents ** - ft_databrowser
‘no’ or ‘yes’, whether to plot event markers. (default is ‘yes’)

** cfg.plotfiltresp ** - ft_preprocessing
‘no’ or ‘yes’, plot filter responses (firws, default = ‘no’)

** cfg.plotfit ** - ft_spike_plot_isi
‘yes’ (default) or ‘no’. This requires that when calling FT_SPIKESTATION_ISI, cfg.gammafit = ‘yes’.

** cfg.plotlabels ** - ft_databrowser
‘yes’, ‘no’ or ‘some’, whether to plot channel labels in vertical viewmode. The option ‘some’ plots one label for every ten channels, which is useful if there are many channels. (default = ‘yes’)

** cfg.plotselection ** - ft_spike_plot_raster
‘yes’ or ‘no’ (default). If yes plot Y axis only for selection in cfg.trials

** cfg.plotunit ** - ft_qualitycheck
scalar, the length of time to be plotted in one panel (default = 3600)

** cfg.point ** - ft_prepare_headmodel

** cfg.polhemus ** - ft_realtime_headlocalizer
filename or mesh, description of the head shape recorded with the Polhemus (default is automatic)

** cfg.polyorder ** - ft_preprocessing
polynome order for poly trend removal (default = 2; note that all lower-order trends will also be removed when using cfg.polyremoval)

** cfg.polyremoval ** - ft_preprocessing
‘no’ or ‘yes’, remove higher order trend from the data (done per trial) (default = ‘no’)

** cfg.polyremoval ** - ft_freqanalysis
number (default = 0), specifying the order of the polynome which is fitted and subtracted from the time domain data prior to the spectral analysis. For example, a value of 1 corresponds to a linear trend. The default is a mean subtraction, thus a value of 0. If no removal is requested, specify -1. see FT_PREPROC_POLYREMOVAL for details

** cfg.position ** - ft_databrowser
location and size of the figure, specified as a vector of the form [left bottom width height].

** cfg.poststim ** - ft_artifact_tms
scalar, time in seconds post onset of detected even to mark as artifactual (default = 0.010 seconds)

** cfg.postwindow ** - ft_interpolatenan
value, length of data after interpolation window, in seconds (default = 1)

** cfg.powmethod ** - ft_sourcedescriptives
‘regular’, ‘lambda1’, ‘trace’, ‘none’

** cfg.precision ** - ft_preprocessing
‘single’ or ‘double’ (default = ‘double’)

** cfg.precision ** - ft_sourcewrite
string, can be ‘single’, ‘double’, etc.

** cfg.preproc.baselinewindow ** - ft_spikedetection, ft_spikedownsample
[begin end] in seconds, the default is the complete trial

** cfg.preproc.baselinewindow ** - ft_databrowser
[begin end] in seconds, the default is the complete trial (default = ‘all’)

** cfg.preproc.boxcar ** - ft_rejectvisual
0.2

** cfg.preproc.bpfiltdir ** - ft_spikedetection, ft_spikedownsample
filter direction, ‘twopass’ (default) or ‘onepass’

** cfg.preproc.bpfilter ** - ft_spikedetection, ft_spikedownsample
‘no’ or ‘yes’ bandpass filter

** cfg.preproc.bpfilter ** - ft_rejectvisual, ft_rejectvisual
‘yes’

** cfg.preproc.bpfilter ** - ft_heartrate
‘yes’ or ‘no’

** cfg.preproc.bpfilter ** - ft_respiration
‘yes’ or ‘no’ (default = ‘yes’)

** cfg.preproc.bpfiltord ** - ft_rejectvisual
4

** cfg.preproc.bpfiltord ** - ft_rejectvisual
8

** cfg.preproc.bpfiltord ** - ft_spikedetection, ft_spikedownsample
bandpass filter order

** cfg.preproc.bpfilttype ** - ft_rejectvisual, ft_rejectvisual
‘but’

** cfg.preproc.bpfilttype ** - ft_spikedetection, ft_spikedownsample
digital filter type, ‘but’ (default) or ‘fir’

** cfg.preproc.bpfreq ** - ft_rejectvisual
[1 15]

** cfg.preproc.bpfreq ** - ft_rejectvisual
[110 140]

** cfg.preproc.bpfreq ** - ft_heartrate, ft_respiration
[low high], filter frequency in Hz

** cfg.preproc.bpfreq ** - ft_spikedetection, ft_spikedownsample
bandpass frequency range, specified as [low high] in Hz

** cfg.preproc.demean ** - ft_spikedetection, ft_spikedownsample
‘no’ or ‘yes’

** cfg.preproc.demean ** - ft_databrowser
‘no’ or ‘yes’, whether to apply baseline correction (default = ‘no’)

** cfg.preproc.detrend ** - ft_spikedetection, ft_spikedownsample
‘no’ or ‘yes’

** cfg.preproc.detrend ** - ft_databrowser
‘no’ or ‘yes’, remove linear trend from the data (done per trial) (default = ‘no’)

** cfg.preproc.dftfilter ** - ft_spikedetection, ft_spikedownsample
‘no’ or ‘yes’ line noise removal using discrete fourier transform

** cfg.preproc.hilbert ** - ft_spikedetection, ft_spikedownsample
‘no’ or ‘yes’

** cfg.preproc.hpfiltdir ** - ft_spikedetection, ft_spikedownsample
filter direction, ‘twopass’ (default) or ‘onepass’

** cfg.preproc.hpfilter ** - ft_spikedetection, ft_spikedownsample
‘no’ or ‘yes’ highpass filter

** cfg.preproc.hpfiltord ** - ft_spikedetection, ft_spikedownsample
highpass filter order

** cfg.preproc.hpfilttype ** - ft_spikedetection, ft_spikedownsample
digital filter type, ‘but’ (default) or ‘fir’

** cfg.preproc.hpfreq ** - ft_spikedetection, ft_spikedownsample
highpass frequency in Hz

** cfg.preproc.lnfilter ** - ft_spikedetection, ft_spikedownsample
‘no’ or ‘yes’ line noise removal using notch filter

** cfg.preproc.lnfiltord ** - ft_spikedetection, ft_spikedownsample
line noise notch filter order

** cfg.preproc.lnfreq ** - ft_spikedetection, ft_spikedownsample
line noise frequency in Hz, default 50Hz

** cfg.preproc.lpfiltdir ** - ft_spikedetection, ft_spikedownsample
filter direction, ‘twopass’ (default) or ‘onepass’

** cfg.preproc.lpfilter ** - ft_spikedetection, ft_spikedownsample
‘no’ or ‘yes’ lowpass filter

** cfg.preproc.lpfilter ** - ft_databrowser
‘no’ or ‘yes’ lowpass filter (default = ‘no’)

** cfg.preproc.lpfiltord ** - ft_spikedetection, ft_spikedownsample
lowpass filter order

** cfg.preproc.lpfilttype ** - ft_spikedetection, ft_spikedownsample
digital filter type, ‘but’ (default) or ‘fir’

** cfg.preproc.lpfreq ** - ft_databrowser, ft_spikedetection, ft_spikedownsample
lowpass frequency in Hz

** cfg.preproc.medianfilter ** - ft_spikedetection, ft_spikedownsample
‘no’ or ‘yes’ jump preserving median filter

** cfg.preproc.medianfiltord ** - ft_spikedetection, ft_spikedownsample
length of median filter

** cfg.preproc.rectify ** - ft_spikedetection, ft_spikedownsample
‘no’ or ‘yes’

** cfg.preproc.rectify ** - ft_rejectvisual, ft_rejectvisual
‘yes’

** cfg.prestim ** - ft_artifact_tms
scalar, time in seconds prior to onset of detected event to mark as artifactual (default = 0.005 seconds)

** cfg.prewindow ** - ft_interpolatenan
value, length of data prior to interpolation window, in seconds (default = 1)

** cfg.projcomb ** - ft_sourceplot
‘mean’, ‘max’, method to combine the different projections

** cfg.projection ** - ft_prepare_layout
string, 2D projection method can be ‘stereographic’, ‘orthographic’, ‘polar’ or ‘gnomic’ (default = ‘polar’) When ‘orthographic’, cfg.viewpoint can be used to indicate to specificy projection (keep empty for legacy projection)

** cfg.projection ** - ft_layoutplot
string, 2D projection method can be ‘stereographic’, ‘ortographic’, ‘polar’, ‘gnomic’ or ‘inverse’ (default = ‘orthographic’)

** cfg.projectmom ** - ft_sourcedescriptives
‘yes’ or ‘no’ (default = ‘no’)

** cfg.projectnoise ** - ft_sourceanalysis
‘no’ or ‘yes’

** cfg.projmethod ** - ft_sourceplot
projection method, how functional volume data is projected onto surface ‘nearest’, ‘project’, ‘sphere_avg’, ‘sphere_weighteddistance’

** cfg.projthresh ** - ft_sourceplot
implements thresholding on the surface level for example, 0.7 means 70% of maximum

** cfg.projvec ** - ft_sourceplot
vector (in mm) to allow different projections that are combined with the method specified in cfg.projcomb

** cfg.projweight ** - ft_sourceplot
vector of weights for the different projections (default = 1)

** cfg.pruneratio ** - ft_megplanar
for singular values, default is 1e-3

** cfg.pseudovalue ** - ft_sourceanalysis
‘no’ or ‘yes’ pseudovalue resampling of trials

** cfg.psth ** - ft_spike_plot_jpsth
‘yes’ (default) or ‘no’. Plot PSTH with JPSTH if ‘yes’;

Q

** cfg.querymethod ** - ft_volumelookup
‘sphere’ searches voxels around the ROI in a sphere (default) = ‘cube’ searches voxels around the ROI in a cube

** cfg.queryrange ** - ft_sourceplot
number, in atlas voxels (default 3)

R

** cfg.radius ** - ft_prepare_headmodel
(optional)

** cfg.radius ** - ft_sourceplot
scalar, maximum radius of cloud (default = 4)

** cfg.randomization ** - ft_sourceanalysis
‘no’ or ‘yes’

** cfg.randomseed ** - ft_connectivitysimulation, ft_dipolesimulation, ft_freqsimulation
‘yes’ or a number or vector with the seed value (default = ‘yes’)

** cfg.randomseed ** - ft_componentanalysis
comp.cfg.callinfo.randomseed (from previous call)

** cfg.randomseed ** - ft_componentanalysis
integer seed value of user’s choice

** cfg.randomseed ** - ft_statistics_montecarlo
string, ‘yes’, ‘no’ or a number (default = ‘yes’)

** cfg.rawtrial ** - ft_sourceanalysis
‘no’ or ‘yes’ construct filter from single trials, apply to single trials. Note that you also may want to set cfg.keeptrials=’yes’ to keep all trial information, especially if using in combination with grid.filter

** cfg.rectify ** - ft_preprocessing
‘no’ or ‘yes’ (default = ‘no’)

** cfg.reducerank ** - ft_dipolefitting, ft_prepare_leadfield, ft_sourceanalysis
‘no’, or number (default = 3 for EEG, 2 for MEG)

** cfg.refchan ** - ft_sourceanalysis
reference channel label (for coherence)

** cfg.refchan ** - ft_realtime_coillocalizer
single string or cell-array with strings

** cfg.refchannel ** - ft_prepare_montage, ft_preprocessing
cell-array with new EEG reference channel(s), this can be ‘all’ for a common average reference

** cfg.refchannel ** - ft_multiplotER, ft_multiplotTFR, ft_singleplotER, ft_singleplotTFR, ft_topoplotER, ft_topoplotTFR
name of reference channel for visualising connectivity, can be ‘gui’

** cfg.refchannel ** - ft_denoise_pca
the channels used as reference signal (default = ‘MEGREF’)

** cfg.refchannel ** - ft_denoise_tsr
the channels used as reference signal (default = ‘MEGREF’), see FT_SELECTDATA

** cfg.refdip ** - ft_sourceanalysis
reference dipole location (for coherence)

** cfg.reflags ** - ft_denoise_tsr
integer array, specifying temporal lags (in msec) by which to shift refchannel with respect to data channels

** cfg.refmethod ** - ft_prepare_montage
‘avg’, ‘bioloar’, ‘comp’ (default = ‘avg’)

** cfg.refmethod ** - ft_preprocessing
‘avg’, ‘median’, or ‘bipolar’ for bipolar derivation of sequential channels (default = ‘avg’)

** cfg.reject ** - ft_regressconfound
vector, [1 X Nconfounds], listing the confounds that are to be rejected (default = ‘all’)

** cfg.rejectonpeak ** - ft_spike_waveform
‘yes’ (default) or ‘no’: takes away waveforms with too late peak, and no rising AP towards peak of other waveforms

** cfg.relnoise ** - ft_dipolesimulation
add noise with level relative to simulated signal

** cfg.remove ** - ft_analysispipeline
cell-array with strings, determines which objects will be removed from the configuration prior to writing it to file. For readibility of the script, you may want to remove the large objectssuch as event structure, trial definition, source positions

** cfg.removefield ** - ft_anonymizedata
cell-array with strings, fields to remove (default = {})

** cfg.removemean ** - ft_timelockanalysis
‘no’ or ‘yes’ for covariance computation (default = ‘yes’)

** cfg.removemean ** - ft_connectivityanalysis
‘yes’ (default), or ‘no’, support for method ‘powcorr’ and ‘amplcorr’.

** cfg.removevalue ** - ft_anonymizedata
cell-array with strings, values to remove (default = {})

** cfg.renderer ** - ft_sourceplot
‘painters’, ‘zbuffer’, ‘ opengl’ or ‘none’ (default = ‘opengl’) note that when using opacity the OpenGL renderer is required.

** cfg.renderer ** - ft_multiplotER, ft_multiplotTFR, ft_singleplotER, ft_singleplotTFR
‘painters’, ‘zbuffer’, ‘ opengl’ or ‘none’ (default = [])

** cfg.renderer ** - ft_databrowser
string, ‘opengl’, ‘zbuffer’, ‘painters’, see MATLAB Figure Properties. If this function crashes, you should try ‘painters’.

** cfg.reref ** - ft_preprocessing
‘no’ or ‘yes’ (default = ‘no’)

** cfg.resample ** - ft_sliceinterp
integer value, default is 1 (for resolution reduction)

** cfg.resample ** - ft_statistics_crossvalidate
true/false; upsample less occurring classes during training and downsample often occurring classes during testing (default = false)

** cfg.resamplefs ** - ft_resampledata
frequency at which the data will be resampled (default = 256 Hz)

** cfg.resolution ** - ft_volumereslice
number, in physical units

** cfg.resolutionmatrix ** - ft_sourcedescriptives
‘yes’ or ‘no’ (default = ‘no’)

** cfg.roi ** - ft_volumelookup, ft_volumelookup
Nx3 vector, coordinates of the POI

** cfg.roi ** - ft_sourceplot
string or cell of strings, region(s) of interest from anatomical atlas (see cfg.atlas above) everything is masked except for ROI

** cfg.roi ** - ft_volumelookup
string or cell-array of strings, ROI from anatomical atlas

** cfg.rotate ** - ft_sliceinterp
number of ccw 90 deg slice rotations (default = 0)

** cfg.rotate ** - ft_layoutplot, ft_prepare_layout
number, rotation around the z-axis in degrees (default = [], which means automatic)

** cfg.round2nearestvoxel ** - ft_volumelookup
‘yes’ or ‘no’ (default = ‘no’), voxel closest to point of interest is calculated and box/sphere is centered around coordinates of that voxel

** cfg.round2nearestvoxel ** - ft_volumelookup
‘yes’ or ‘no’, voxel closest to POI is calculated (default = ‘yes’)

** cfg.runica.anneal ** - ft_componentanalysis

** cfg.runica.annealdeg ** - ft_componentanalysis

** cfg.runica.bias ** - ft_componentanalysis

** cfg.runica.block ** - ft_componentanalysis

** cfg.runica.extended ** - ft_componentanalysis

** cfg.runica.interput ** - ft_componentanalysis

** cfg.runica.logfile ** - ft_componentanalysis

** cfg.runica.lrate ** - ft_componentanalysis

** cfg.runica.maxsteps ** - ft_componentanalysis

** cfg.runica.momentum ** - ft_componentanalysis

** cfg.runica.pca ** - ft_componentanalysis

** cfg.runica.posact ** - ft_componentanalysis

** cfg.runica.specgram ** - ft_componentanalysis

** cfg.runica.sphering ** - ft_componentanalysis

** cfg.runica.stop ** - ft_componentanalysis

** cfg.runica.verbose ** - ft_componentanalysis

** cfg.runica.weights ** - ft_componentanalysis

S

** cfg.s1.ampl ** - ft_freqsimulation
amplitude of signal 1

** cfg.s1.ampl ** - ft_timelocksimulation
number (default = 1.0)

** cfg.s1.freq ** - ft_freqsimulation
frequency of signal 1

** cfg.s1.numcycli ** - ft_timelocksimulation
number (default = 1)

** cfg.s1.phase ** - ft_freqsimulation
phase (in rad) relative to cosine of signal 1 (default depends on method) = number or ‘random’

** cfg.s2.ampl ** - ft_freqsimulation
amplitude of signal 2

** cfg.s2.ampl ** - ft_timelocksimulation
number (default = 0.7)

** cfg.s2.freq ** - ft_freqsimulation
frequency of signal 2

** cfg.s2.numcycli ** - ft_timelocksimulation
number (default = 2)

** cfg.s2.phase ** - ft_freqsimulation
phase (in rad) relative to cosine of signal 1 (default depends on method) = number or ‘random’

** cfg.s3.ampl ** - ft_freqsimulation
amplitude of signal 3

** cfg.s3.ampl ** - ft_timelocksimulation
number (default = 0.2)

** cfg.s3.freq ** - ft_freqsimulation
frequency of signal 3

** cfg.s3.numcycli ** - ft_timelocksimulation
number (default = 4)

** cfg.s3.phase ** - ft_freqsimulation
phase (in rad) relative to cosine of signal 1 (default depends on method) = number or ‘random’

** cfg.s4.ampl ** - ft_freqsimulation
amplitude of signal 4

** cfg.s4.freq ** - ft_freqsimulation
frequency of signal 4

** cfg.s4.phase ** - ft_freqsimulation
phase (in rad) relative to cosine of signal 1 (default depends on method) = number or ‘random’

** cfg.samperframe ** - ft_movieplotER, ft_movieplotTFR
number, samples per fram (default = 1)

** cfg.sampleindex ** - ft_resampledata
‘no’ or ‘yes’, add a channel with the original sample indices (default = ‘no’)

** cfg.saveaspng ** - ft_clusterplot
string, filename of the output figures (default = ‘no’)

** cfg.savemat ** - ft_qualitycheck
string, ‘yes’ or ‘no’ to save the analysis (default = ‘yes’)

** cfg.saveplot ** - ft_qualitycheck
string, ‘yes’ or ‘no’ to save the visualization (default = ‘yes’)

** cfg.scalar ** - ft_math
scalar value to be used in the operation

** cfg.scale ** - ft_defacemesh, ft_defacevolume
initial size of the box along each dimension (default is automatic)

** cfg.scale ** - ft_channelnormalise
scalar value used for scaling (default = 1)

** cfg.scaling ** - ft_volumewrite
‘yes’ or ‘no’

** cfg.scalpsmooth ** - ft_volumesegment
‘no’, or scalar, the FWHM of the gaussian kernel in voxels, (default = 5)

** cfg.scalpthreshold ** - ft_volumesegment
‘no’, or scalar, relative threshold value which is used to threshold the anatomical data in order to create a volumetric scalpmask (see below), (default = 0.1)

** cfg.scatter ** - ft_spike_plot_isireturn
‘yes’ (default) or ‘no’. If ‘yes’, we plot the individual values.

** cfg.searchrange ** - ft_recodeevent
‘anywhere’ search anywhere for the event, (default) ‘insidetrial’ only search inside ‘outsidetrial’ only search outside ‘beforetrial’ only search before the trial ‘aftertrial’ only search after the trial ‘beforezero’ only search before time t=0 of each trial ‘afterzero’ only search after time t=0 of each trial

** cfg.selcfg ** - ft_databrowser
configuration options for function in cfg.selfun

** cfg.seldat ** - ft_databrowser
‘selected’ or ‘all’, specifies whether only the currently selected or all channels will be passed to the selfun (default = ‘selected’)

** cfg.selectfeature ** - ft_databrowser
string, name of feature to be selected/added (default = ‘visual’)

** cfg.selection ** - ft_defacemesh, ft_defacevolume
which voxels to keep, can be ‘inside’ or ‘outside’ (default = ‘outside’)

** cfg.selectmode ** - ft_databrowser
‘markartifact’, ‘markpeakevent’, ‘marktroughevent’ (default = ‘markartifact’)

** cfg.selfun ** - ft_databrowser
string, name of function that is evaluated using the right-click context menu. The selected data and cfg.selcfg are passed on to this function.

** cfg.serial ** - ft_omri_quality
serial port (default = /dev/ttyS0), set [] to disable motion reporting

** cfg.shading ** - ft_topoplotIC
‘flat’ ‘interp’ (default = ‘flat’)

** cfg.shading ** - ft_topoplotER, ft_topoplotTFR
‘flat’ or ‘interp’ (default = ‘flat’)

** cfg.shaft.along ** - ft_electrodeplacement
1x3 or Nx3 positions along the shaft

** cfg.shaft.distance ** - ft_electrodeplacement
scalar, distance between electrodes

** cfg.shaft.tip ** - ft_electrodeplacement
1x3 position of the electrode at the tip of the shaft

** cfg.showRawVariation ** - ft_omri_quality
1 to show variation in raw scans (default), 0 to show var. in processed scans

** cfg.showcomment ** - ft_multiplotER
‘yes’ or ‘no’ (default = ‘yes’)

** cfg.showcomment ** - ft_multiplotTFR
‘yes’, ‘no’ (default = ‘yes’)

** cfg.showinfo ** - ft_analysispipeline
string or cell array of strings, information to display in the gui boxes, can be any combination of ‘functionname’, ‘revision’, ‘matlabversion’, ‘computername’, ‘username’, ‘calltime’, ‘timeused’, ‘memused’, ‘workingdir’, ‘scriptpath’ (default = ‘functionname’, only display function name). Can also be ‘all’, show all pipeline. Please note that if you want to show a lot of information, this will require a lot of screen real estate.

** cfg.showlabels ** - ft_multiplotER
‘yes’ or ‘no’ (default = ‘no’)

** cfg.showlabels ** - ft_multiplotTFR
‘yes’, ‘no’ (default = ‘no’)

** cfg.showoutline ** - ft_multiplotER
‘yes’ or ‘no’ (default = ‘no’)

** cfg.showoutline ** - ft_multiplotTFR
‘yes’, ‘no’ (default = ‘no’)

** cfg.showscale ** - ft_multiplotER
‘yes’ or ‘no’ (default = ‘yes’)

** cfg.showscale ** - ft_multiplotTFR
‘yes’, ‘no’ (default = ‘yes’)

** cfg.singleshell.batchsize ** - ft_prepare_leadfield
scalar or ‘all’ (default 1), number of dipoles for which the leadfield is computed in a single call to the low-level code. Trades off memory efficiency for speed.

** cfg.skipcomnt ** - ft_prepare_layout
‘yes’ or ‘no’, whether the comment should be included in the layout or not (default = ‘no’)

** cfg.skipscale ** - ft_prepare_layout
‘yes’ or ‘no’, whether the scale should be included in the layout or not (default = ‘no’)

** cfg.skullsmooth ** - ft_volumesegment
‘no’, or scalar, the FWHM of the gaussian kernel in voxels, (default = 5) this parameter is only used when the segmentation contains 6 tisuse types, including ‘bone’

** cfg.skullthreshold ** - ft_volumesegment
‘no’, or scalar, relative threshold value which is used to threshold the anatomical data in order to create a volumetric scalpmask (see below), (default = 0.5). this parameter is only used when the segmetnation contains 6 tissue types, including ‘bone’,

** cfg.slice ** - ft_sourceplot
requires ‘anatomical’ as input (default = ‘none’) ‘2d’, plots 2D slices through the cloud with an outline of the mesh ‘3d’, draws an outline around the mesh at a particular slice

** cfg.slicedim ** - ft_sourceplot
dimension to slice 1 (x-axis) 2(y-axis) 3(z-axis) (default = 3)

** cfg.slicepos ** - ft_sourceplot
‘auto’ or Nx1 vector specifying the position of the slice plane along the orientation axis (default = ‘auto’: chooses slice(s) with the most data)

** cfg.slicerange ** - ft_sourceplot
range of slices in data, (default = ‘auto’) ‘auto’, full range of data [min max], coordinates of first and last slice in voxels

** cfg.smooth ** - ft_defacevolume, ft_volumedownsample
‘no’ or the FWHM of the gaussian kernel in voxels (default = ‘no’)

** cfg.smooth ** - ft_prepare_sourcemodel
5, smoothing in voxels

** cfg.smoothFWHM ** - ft_omri_pipeline
kernel width in mm (Full Width Half Maximum) for smoothing (default = 0 => no smoothing)

** cfg.smoothFWHM ** - ft_omri_pipeline_nuisance
kernel width in mm (Full Width Half Maximum) for smoothing (default = 8)

** cfg.snapshot ** - ft_volumerealign
‘no’ (‘yes’), making a snapshot of the image once a fiducial or landmark location is selected. The optional second output argument to the function will contain the handles to these figures.

** cfg.snapshotfile ** - ft_volumerealign
‘ft_volumerealign_snapshot’ or string, the root of the filename for the snapshots, including the path. If no path is given the files are saved to the pwd. The consecutive figures will be numbered and saved as png-file.

** cfg.sobi.n_sources ** - ft_componentanalysis

** cfg.sobi.p_correlations ** - ft_componentanalysis

** cfg.spacemax ** - ft_sliceinterp
‘auto’ (default) or integer (last slice position)

** cfg.spacemin ** - ft_sliceinterp
‘auto’ (default) or integer (first slice position)

** cfg.sphere ** - ft_volumelookup
radius of each sphere in cm/mm dep on unit of input

** cfg.spheremesh ** - ft_megplanar, ft_megrealign
number of dipoles in the source layer (default = 642)

** cfg.sphereradius ** - ft_sourceplot
maximum distance from each voxel to the surface to be included in the sphere projection methods, expressed in mm

** cfg.spherify ** - ft_prepare_sourcemodel
‘yes’ or ‘no’, scale the source model so that it fits inside a sperical volume conduction model (default = ‘no’)

** cfg.spikechannel ** - ft_spike_select, ft_spike_waveform
See FT_CHANNELSELECTION for details.

** cfg.spikechannel ** - ft_spike_psth
See FT_CHANNELSELECTION for details. cfg.trials is vector of indices (e.g., 1:2:10) logical selection of trials (e.g., [1010101010]) ‘all’ (default), selects all trials

** cfg.spikechannel ** - ft_spikedensity
cell-array ,see FT_CHANNELSELECTION for details

** cfg.spikechannel ** - ft_spiketriggeredspectrum_stat
label of ONE unit, according to FT_CHANNELSELECTION

** cfg.spikechannel ** - ft_spike_plot_raster, ft_spike_rate
see FT_CHANNELSELECTION for details

** cfg.spikechannel ** - ft_spike_plot_isireturn, ft_spike_plot_psth
string or index of single spike channel to trigger on (default = 1) Only one spikechannel can be plotted at a time.

** cfg.spikechannel ** - ft_spike_isi
string or index of spike channels to trigger on (default = ‘all’) See FT_CHANNELSELECTION for details.

** cfg.spikechannel ** - ft_spike_plot_isi
string or index or logical array to to select 1 spike channel. (default = 1).

** cfg.spikechannel ** - ft_spiketriggeredaverage, ft_spiketriggeredinterpolation
string, name of single spike channel to trigger on

** cfg.spikechannel ** - ft_spiketriggeredspectrum_fft
string, name of spike channels to trigger on cfg.channel = Nx1 cell-array with selection of channels (default = ‘all’), see FT_CHANNELSELECTION for details

** cfg.spikelength ** - ft_spike_plot_raster
number >0 and <=1 indicating the length of the spike. If cfg.spikelength = 1, then no space will be left between subsequent rows representing trials (row-unit is 1).

** cfg.spikesel ** - ft_spiketriggeredspectrum_stat
‘all’ (default) or numerical or logical selection of spikes.

** cfg.spm.cost_fun ** - ft_volumerealign
cost function string: ‘mi’ - Mutual Information (default) ‘nmi’ - Normalised Mutual Information ‘ecc’ - Entropy Correlation Coefficient ‘ncc’ - Normalised Cross Correlation

** cfg.spm.fwhm ** - ft_volumerealign
smoothing to apply to 256x256 joint histogram, default: [7 7]

** cfg.spm.params ** - ft_volumerealign
starting estimates (6 elements), default: [0 0 0 0 0 0]

** cfg.spm.regtype ** - ft_volumerealign
‘subj’, ‘rigid’

** cfg.spm.sep ** - ft_volumerealign
optimisation sampling steps (mm), default: [4 2]

** cfg.spm.smoref ** - ft_volumerealign
scalar value

** cfg.spm.smosrc ** - ft_volumerealign
scalar value

** cfg.spm.tol ** - ft_volumerealign
tolerences for accuracy of each param, default: [0.02 0.02 0.02 0.001 0.001 0.001]

** cfg.spmmethod ** - ft_volumesegment
string, ‘old’, ‘new’, ‘mars’ (default = ‘old’). This pertains to the algorithm used when cfg.spmversion=’spm12’, see below.

** cfg.spmversion ** - ft_volumesegment
string, ‘spm2’, ‘spm8’, ‘spm12’ (default = ‘spm12’)

** cfg.spmversion ** - ft_prepare_mesh, ft_prepare_sourcemodel, ft_volumedownsample, ft_volumenormalise, ft_volumerealign
string, ‘spm2’, ‘spm8’, ‘spm12’ (default = ‘spm8’)

** cfg.spmversion ** - ft_volumebiascorrect
string, ‘spm8’, ‘spm12’ (default = ‘spm8’)

** cfg.standardisedata ** - ft_denoise_tsr
string, ‘yes’ or ‘no’, whether or not to standardise dependent variable prior to the regression (default = ‘no’)

** cfg.standardiserefdata ** - ft_denoise_tsr
string, ‘yes’ or ‘no’, whether or not to standardise reference data prior to the regression (default = ‘no’)

** cfg.statistic ** - ft_statistics_analytic, ft_statistics_montecarlo
‘indepsamplesT’ independent samples T-statistic, ‘indepsamplesF’ independent samples F-statistic, ‘indepsamplesregrT’ independent samples regression coefficient T-statistic, ‘indepsamplesZcoh’ independent samples Z-statistic for coherence, ‘depsamplesT’ dependent samples T-statistic, ‘depsamplesFmultivariate’ dependent samples F-statistic MANOVA, ‘depsamplesregrT’ dependent samples regression coefficient T-statistic, ‘actvsblT’ activation versus baseline T-statistic.

** cfg.statistic ** - ft_statistics_stats
‘ttest’ test against a mean of zero ‘ttest2’ compare the mean in two conditions ‘paired-ttest’ ‘anova1’ ‘kruskalwallis’ ‘signtest’ ‘signrank’ ‘pearson’ ‘kendall’ ‘spearman’

** cfg.statistic ** - ft_statistics_crossvalidate
a cell-array of statistics to report (default = {‘accuracy’ ‘binomial’})

** cfg.statistic ** - ft_statistics_analytic
string, statistic to compute for each sample or voxel (see below)

** cfg.stimuli ** - ft_spike_rate_orituning
should be an 1 x nConditions array of orientations or directions in radians varargin{i} corresponds to cfg.stimuli(i)

** cfg.stimulus1.isi ** - ft_steadystatesimulation
in seconds, i.e. for 10Hz you would specify 0.1 seconds as the interstimulus interval (default = 0.1176)

** cfg.stimulus1.isijitter ** - ft_steadystatesimulation
in seconds, max jitter relative to the previous stimulus (default = 0)

** cfg.stimulus1.kernelduration ** - ft_steadystatesimulation
in seconds (default = isi)

** cfg.stimulus1.kernelshape ** - ft_steadystatesimulation
‘sine’

** cfg.stimulus1.mode ** - ft_steadystatesimulation
‘periodic’, ‘transient’ or ‘off’ (default = ‘periodic’)

** cfg.stimulus1.number ** - ft_steadystatesimulation
does not apply for periodic stimuli

** cfg.stimulus1.onset ** - ft_steadystatesimulation
in seconds, first stimulus relative to the start of the trial (default = 0)

** cfg.stimulus1.onsetjitter ** - ft_steadystatesimulation
in seconds, max jitter that is added to the onset (default = 0)

** cfg.stimulus2.condition ** - ft_steadystatesimulation
1xM vector with condition codes for each transient within a trial (default = [1 1 2 2])

** cfg.stimulus2.condition ** - ft_steadystatesimulation
does not apply for periodic stimuli

** cfg.stimulus2.gain ** - ft_steadystatesimulation
1xM vector with gain for each condition for each transient within a trial(default = [1 1 1 1])

** cfg.stimulus2.gain ** - ft_steadystatesimulation
does not apply for periodic stimuli

** cfg.stimulus2.isi ** - ft_steadystatesimulation
in seconds as the interstimulus interval (default = 0.7)

** cfg.stimulus2.isijitter ** - ft_steadystatesimulation
in seconds, max jitter relative to the previous stimulus ((default = 0.2)

** cfg.stimulus2.kernelduration ** - ft_steadystatesimulation
in seconds (default = 0.75*isi)

** cfg.stimulus2.kernelshape ** - ft_steadystatesimulation
‘hanning’

** cfg.stimulus2.mode ** - ft_steadystatesimulation
‘periodic’, ‘transient’ or ‘off’ (default = ‘transient’)

** cfg.stimulus2.number ** - ft_steadystatesimulation
scalar M, how many transients are to be presented per trial (default = 4)

** cfg.stimulus2.onset ** - ft_steadystatesimulation
in seconds, first stimulus relative to the start of the trial (default = 0.7)

** cfg.stimulus2.onsetjitter ** - ft_steadystatesimulation
in seconds, max jitter that is added to the onset (default = 0.2)

** cfg.style ** - ft_topoplotER, ft_topoplotIC, ft_topoplotTFR
plot style (default = ‘both’) ‘straight’ colormap only ‘contour’ contour lines only ‘both’ (default) both colormap and contour lines ‘fill’ constant color between lines ‘blank’ only the head shape

** cfg.submethod ** - ft_prepare_headmodel
(optional)

** cfg.subplotsize ** - ft_clusterplot
layout of subplots ([h w], default [3 5])

** cfg.supchan ** - ft_sourceanalysis
suppressed channel label(s)

** cfg.supdip ** - ft_sourceanalysis
suppressed dipole location(s)

** cfg.supmethod ** - ft_sourcedescriptives
‘chan_dip’, ‘chan’, ‘dip’, ‘none’ (default)

** cfg.surfdownsample ** - ft_sourceplot
number (default = 1, i.e. no downsampling)

** cfg.surffile ** - ft_sourceplot
string, file that contains the surface (default = ‘surface_white_both.mat’) ‘surface_white_both.mat’ contains a triangulation that corresponds with the SPM anatomical template in MNI coordinates

** cfg.surfinflated ** - ft_sourceplot
string, file that contains the inflated surface (default = []) may require specifying a point-matching (uninflated) surffile

** cfg.symmetry ** - ft_dipolefitting, ft_prepare_sourcemodel
‘x’, ‘y’ or ‘z’ symmetry for two dipoles, can be empty (default = [])

T

** cfg.t_ftimwin ** - ft_mvaranalysis
the width of the sliding window on which the coefficients are estimated

** cfg.tail ** - ft_statistics_analytic, ft_statistics_montecarlo, ft_statistics_stats
number, -1, 1 or 0 (default = 0)

** cfg.taper ** - ft_freqanalysis
‘dpss’, ‘hanning’ or many others, see WINDOW (default = ‘dpss’) For cfg.output=’powandcsd’, you should specify the channel combinations between which to compute the cross-spectra as cfg.channelcmb. Otherwise you should specify only the channels in cfg.channel.

** cfg.taper ** - ft_spiketriggeredspectrum_fft
‘dpss’, ‘hanning’ or many others, see WINDOW (default = ‘hanning’)

** cfg.tapsmofrq ** - ft_freqanalysis
number, the amount of spectral smoothing through multi-tapering. Note that 4 Hz smoothing means plus-minus 4 Hz, i.e. a 8 Hz smoothing box.

** cfg.tapsmofrq ** - ft_spiketriggeredspectrum_fft
number, the amount of spectral smoothing through multi-tapering. Note that 4 Hz smoothing means plus-minus 4 Hz, i.e. a 8 Hz smoothing box. Note: multitapering rotates phases (no problem for consistency)

** cfg.tapsmofrq ** - ft_freqanalysis
vector 1 x numfoi, the amount of spectral smoothing through multi-tapering. Note that 4 Hz smoothing means plus-minus 4 Hz, i.e. a 8 Hz smoothing box. cfg.foi = vector 1 x numfoi, frequencies of interest cfg.taper = ‘dpss’, ‘hanning’ or many others, see WINDOW (default = ‘dpss’) For cfg.output=’powandcsd’, you should specify the channel combinations between which to compute the cross-spectra as cfg.channelcmb. Otherwise you should specify only the channels in cfg.channel. cfg.t_ftimwin = vector 1 x numfoi, length of time window (in seconds) cfg.toi = vector 1 x numtoi, the times on which the analysis windows should be centered (in seconds), or a string such as ‘50%’ or ‘all’ (default). Both string options use all timepoints available in the data, but ‘all’ centers a spectral estimate on each sample, whereas the percentage specifies the degree of overlap between the shortest time windows from cfg.t_ftimwin.

** cfg.tapsmofrq ** - ft_spiketriggeredspectrum_convol
vector 1 x numfoi, the amount of spectral smoothing through multi-tapering. Note that 4 Hz smoothing means plus-minus 4 Hz, i.e. a 8 Hz smoothing box. cfg.foi = vector 1 x numfoi, frequencies of interest cfg.taper = ‘dpss’, ‘hanning’ or many others, see WINDOW (default = ‘hanning’) cfg.t_ftimwin = vector 1 x numfoi, length of time window (in seconds) cfg.taperopt = parameter that goes in WINDOW function (only applies to windows like KAISER). cfg.spikechannel = cell-array with selection of channels (default = ‘all’) see FT_CHANNELSELECTION for details cfg.channel = Nx1 cell-array with selection of channels (default = ‘all’), see FT_CHANNELSELECTION for details cfg.borderspikes = ‘yes’ (default) or ‘no’. If ‘yes’, we process the spikes falling at the border using an LFP that is not centered on the spike. If ‘no’, we output NaNs for spikes around which we could not center an LFP segment. cfg.rejectsaturation= ‘yes’ (default) or ‘no’. If ‘yes’, we set EEG segments where the maximum or minimum voltage range is reached with zero derivative (i.e., saturated signal) to NaN, effectively setting all spikes phases that use these parts of the EEG to NaN. An EEG that saturates always returns the same phase at all frequencies and should be ignored.

** cfg.target ** - ft_electroderealign
list of electrode sets that will be averaged

** cfg.target ** - ft_electroderealign
single electrode set that serves as standard

** cfg.target.label ** - ft_electroderealign
{‘NAS’, ‘LPA’, ‘RPA’}

** cfg.target.pos ** - ft_electroderealign
[0 -90 0] % location of the right ear

** cfg.target.pos ** - ft_electroderealign
[0 90 0] % location of the left ear

** cfg.target.pos ** - ft_electroderealign
[110 0 0] % location of the nose

** cfg.template ** - ft_megrealign

** cfg.template ** - ft_megrealign
datasets that are averaged into the standard

** cfg.template ** - ft_volumesegment
filename of the template anatomical MRI (default = ‘/spm2/templates/T1.mnc’ or ‘/spm8/templates/T1.nii’)

** cfg.template ** - ft_prepare_neighbours
name of the template file, e.g. CTF275_neighb.mat

** cfg.template ** - ft_megrealign
single dataset that serves as template

** cfg.template ** - ft_volumenormalise
string, filename of the template anatomical MRI (default = ‘T1.mnc’ for spm2 or ‘T1.nii’ for spm8)

** cfg.template ** - ft_realtime_headlocalizer
string, name of a template dataset for between-session repositioning (default = [])

** cfg.template.axes ** - ft_interactiverealign
string, ‘yes’ or ‘no (default = ‘no’)

** cfg.template.elec ** - ft_interactiverealign
structure

** cfg.template.grad ** - ft_interactiverealign
structure

** cfg.template.headmodel ** - ft_interactiverealign
structure, see FT_PREPARE_HEADMODEL

** cfg.template.headmodelstyle ** - ft_interactiverealign
‘vertex’, ‘edge’, ‘surface’ or ‘both’ (default = ‘edge’)

** cfg.template.headshape ** - ft_interactiverealign
structure, see FT_READ_HEADSHAPE

** cfg.template.headshapestyle ** - ft_interactiverealign
‘vertex’, ‘edge’, ‘surface’ or ‘both’ (default = ‘vertex’)

** cfg.template.mri ** - ft_interactiverealign
structure, see FT_READ_MRI

** cfg.testtrials ** - ft_denoise_tsr
cell array or string, trial indices to be used as test folds in a cross-validation scheme (numel(cfg.testrials == number of folds))

** cfg.threshold ** - ft_prepare_sourcemodel
0.1, relative to the maximum value in the segmentation

** cfg.threshold ** - ft_denoise_tsr
integer array, ([1 by 2] or [1 by numel(cfg.channel) + numel(cfg.reflags)]), regularization or shrinkage (‘lambda’) parameter to be loaded on the diagonal of the penalty term (if cfg.method == ‘mlrridge’ or ‘mlrqridge’)

** cfg.threshold ** - ft_heartrate
scalar, between 0 and 1 (default = 0.4)

** cfg.time ** - ft_resampledata
cell-array with one time axis per trial (i.e. from another dataset)

** cfg.time ** - ft_freqsimulation
cell-array with one time axis per trial, which are for example obtained from an existing dataset

** cfg.timestampdefinition ** - ft_spikedetection, ft_spikedownsample
‘orig’ or ‘sample’

** cfg.timestampspersecond ** - ft_spike_maketrials
number of timestaps per second (for Neuralynx, 1000000 for example). This can be computed for example from the LFP hdr (cfg.timestampspersecond = data.hdr.Fs*data.hdr.TimeStampPerSecond) or is a priori known.

** cfg.timwin ** - ft_nonlinearassociation
0.2

** cfg.timwin ** - ft_spiketriggeredinterpolation
[begin end], duration of LFP segment around each spike (default = [-0.005 0.005]) to be removed

** cfg.timwin ** - ft_spiketriggeredaverage, ft_spiketriggeredspectrum_fft
[begin end], time around each spike (default = [-0.1 0.1])

** cfg.timwin ** - ft_spiketriggeredspectrum_stat
double or ‘all’ (default) - double: indicates we compute statistic with a sliding window of cfg.timwin, i.e. time-resolved analysis. - ‘all’: we compute statistic over all time-points, i.e. in non-time resolved fashion.

** cfg.tissue ** - ft_prepare_headmodel

** cfg.tissue ** - ft_prepare_headmodel
a string or integer, to be used in combination with a ‘seg’ for the second intput. If ‘brain’, ‘skull’, and ‘scalp’ are fields present in ‘seg’, then cfg.tissue need not be specified, as these are defaults, depending on cfg.method. Otherwise, cfg.tissue should refer to which field(s) of seg should be used.

** cfg.tissue ** - ft_prepare_mesh
cell-array with tissue types or numeric vector with integer values

** cfg.tissue ** - ft_prepare_headmodel, ft_prepare_headmodel
see above; in combination with ‘seg’ input

** cfg.tissue ** - ft_prepare_headmodel, ft_prepare_headmodel
see above; in combination with ‘seg’ input; default options are ‘brain’ or ‘scalp’

** cfg.tissue ** - ft_prepare_headmodel
see above; in combination with ‘seg’ input; default options are ‘brain’ or ‘scalp’; must be only 1 value

** cfg.tissue ** - ft_prepare_mesh
{‘scalp’, ‘skull’, ‘brain’};

** cfg.tissueval ** - ft_prepare_headmodel

** cfg.title ** - ft_sliceinterp
optional title (default is ‘’)

** cfg.title ** - ft_topoplotIC
string or ‘auto’ or ‘off’, specify a figure title, or use ‘component N’ (auto) as the title

** cfg.title ** - ft_singleplotER, ft_singleplotTFR
string, title of plot

** cfg.title ** - ft_sourceplot
string, title of the plot

** cfg.toi ** - ft_nonlinearassociation
[]

** cfg.toi ** - ft_mvaranalysis
[t1 t2 … tx] the time points at which the windows are centered

** cfg.toi ** - ft_freqanalysis
vector 1 x numtoi, the times on which the analysis windows should be centered (in seconds)

** cfg.toilim ** - ft_freqgrandaverage
[tmin tmax] or ‘all’, to specify a subset of latencies (default = ‘all’)

** cfg.toilim ** - ft_redefinetrial
[tmin tmax] to specify a latency window in seconds, can be Nx2 vector

** cfg.tolerance ** - ft_appendfreq
scalar, tolerance to determine how different the frequency and/or time axes are allowed to still be considered compatible (default = 1e-5)

** cfg.tolerance ** - ft_appendtimelock
scalar, tolerance to determine how different the time axes are allowed to still be considered compatible (default = 1e-5)

** cfg.topolabel ** - ft_componentanalysis
Nx1 cell-array with the channel labels

** cfg.topplotfunc ** - ft_spike_plot_raster
‘bar’ (default) or ‘line’.

** cfg.topplotsize ** - ft_spike_plot_raster
number ranging from 0 to 1, indicating the proportion of the rasterplot that the top plot will take (e.g., with 0.7 the top plot will be 70% of the rasterplot in size). Default = 0.5.

** cfg.tpm ** - ft_volumesegment
cell-array containing the filenames of the tissue probability maps

** cfg.transform ** - ft_prepare_headmodel

** cfg.translate ** - ft_defacemesh, ft_defacevolume
initial position of the center of the box (default = [0 0 0])

** cfg.translate ** - ft_defacemesh, ft_defacevolume
initial rotation of the box (default = [0 0 0])

** cfg.trialborders ** - ft_spike_plot_raster
‘yes’ or ‘no’. If ‘yes’, borders of trials are plotted

** cfg.trialdef ** - ft_definetrial
structure with details of trial definition, see below

** cfg.trialdef.eventtype ** - ft_artifact_tms, ft_definetrial
‘string’

** cfg.trialdef.eventvalue ** - ft_artifact_tms, ft_definetrial
number, string or list with numbers or strings

** cfg.trialdef.poststim ** - ft_definetrial
number, latency in seconds (optional)

** cfg.trialdef.prestim ** - ft_definetrial
number, latency in seconds (optional)

** cfg.trialdef.triallength ** - ft_definetrial
duration in seconds (can also be 1 or Inf) cfg.trialdef.ntrials = number of trials (can also be 1 or Inf)

** cfg.trialfun ** - ft_artifact_tms
function name, see below (default = ‘ft_trialfun_general’)

** cfg.trialfun ** - ft_definetrial
string with function name, see below (default = ‘ft_trialfun_general’)

** cfg.trialfun ** - ft_realtime_oddball
string with the trial function

** cfg.triallength ** - ft_connectivitysimulation
in seconds

** cfg.triallength ** - ft_dipolesimulation
time in seconds

** cfg.trials ** - ft_spike_jpsth
‘all’ (default) or numerical or logical array of to be selected trials.

** cfg.trials ** - ft_channelnormalise, ft_channelrepair, ft_componentanalysis, ft_denoise_dssp, ft_denoise_synthetic, ft_detect_movement, ft_freqanalysis, ft_freqdescriptives, ft_megplanar, ft_multiplotER, ft_multiplotTFR, ft_nonlinearassociation, ft_preprocessing, ft_redefinetrial, ft_rejectvisual, ft_resampledata, ft_scalpcurrentdensity, ft_singleplotTFR, ft_timelockanalysis, ft_topoplotER, ft_topoplotTFR
‘all’ or a selection given as a 1xN vector (default = ‘all’)

** cfg.trials ** - ft_singleplotER
‘all’ or a selection given as a 1xn vector (default = ‘all’)

** cfg.trials ** - ft_connectivityanalysis
Nx1 vector specifying which trials to include for the computation. This only has an effect when the input data contains repetitions.

** cfg.trials ** - ft_denoise_tsr
integer array, trials to be used in regression, see FT_SELECTDATA

** cfg.trials ** - ft_denoise_pca
list of trials that are used (default = ‘all’)

** cfg.trials ** - ft_spike_psth, ft_spikedensity
numeric or logical selection of trials (default = ‘all’)

** cfg.trials ** - ft_spike_plot_raster
numeric or logical selection of trials (default = ‘all’).

** cfg.trials ** - ft_spike_isi, ft_spike_xcorr
numeric selection of trials (default = ‘all’)

** cfg.trials ** - ft_spike_select
vector of indices (e.g., 1:2:10) logical selection of trials (e.g., [1010101010]) ‘all’ (default), selects all trials

** cfg.trials ** - ft_spike_rate
vector of indices (e.g., 1:2:10) logical selection of trials (e.g., [1010101010]) ‘all’ (default), selects all trials% cfg.trials

** cfg.trials ** - ft_spiketriggeredspectrum_stat
vector of indices (e.g., 1:2:10), logical selection of trials (e.g., [1010101010]), or ‘all’ (default)

** cfg.trl ** - ft_preprocessing, ft_redefinetrial
Nx3 matrix with the trial definition, see FT_DEFINETRIAL

** cfg.trl ** - ft_audiovideobrowser
Nx3 matrix, see FT_DEFINETRIAL

** cfg.trl ** - ft_headmovement
empty (default), or Nx3 matrix with the trial definition, can be empty.see FT_DEFINETRIAL. If defined empty, the whole recording is used

** cfg.trl ** - ft_spike_maketrials
is an nTrials-by-M matrix, with at least 3 columns: Every row contains start (col 1), end (col 2) and offset of the event trigger in the trial in timestamp or sample units (cfg.trlunit). For example, an offset of -1000 means that the trigger (t = 0 sec) occurred 1000 timestamps or samples after the trial start. If more columns are added than 3, these are used to construct the spike.trialinfo field having information about the trial. Note that values in cfg.trl get inaccurate above 2^53 (in that case it is better to use the original uint64 representation)

** cfg.trl ** - ft_databrowser
structure that defines the data segments of interest, only applicable for trial-based data

** cfg.trl ** - ft_artifact_threshold
structure that defines the data segments of interest, see FT_DEFINETRIAL

** cfg.trl ** - ft_artifact_ecg, ft_artifact_eog, ft_artifact_jump, ft_artifact_muscle, ft_artifact_tms, ft_artifact_zvalue
structure that defines the data segments of interest. See FT_DEFINETRIAL

** cfg.trllen ** - ft_freqsimulation
length of simulated trials in seconds

** cfg.trllen ** - ft_timelocksimulation
length of simulated trials in seconds (default = 1)

** cfg.trlunit ** - ft_spike_maketrials
‘timestamps’ (default) or ‘samples’. If ‘samples’, cfg.trl should be specified in samples, and cfg.hdr = data.hdr should be specified. This option can be used to reuse a cfg.trl that was used for preprocessing LFP data. If ‘timestamps’, cfg.timestampspersecond should be specified, but cfg.hdr should not.

** cfg.truncate ** - ft_denoise_pca
optional truncation of the singular value spectrum (default = ‘no’)

U

** cfg.unit ** - ft_prepare_headmodel

** cfg.unmixing ** - ft_componentanalysis
NxN unmixing matrix

** cfg.updatesens ** - ft_combineplanar, ft_componentanalysis, ft_denoise_pca, ft_rejectcomponent
‘no’ or ‘yes’ (default = ‘yes’)

** cfg.updatesens ** - ft_denoise_tsr
string, ‘yes’ or ‘no’ (default = ‘yes’)

** cfg.usefftfilt ** - ft_preprocessing
‘no’ or ‘yes’, use fftfilt instead of filter (firws, default = ‘no’)

** cfg.uvar ** - ft_statistics_analytic, ft_statistics_montecarlo
number or list with indices, unit variable(s)

V

** cfg.variance ** - ft_freqdescriptives
‘yes’ or ‘no’, estimate standard error in the standard way (default = ‘no’)

** cfg.vartriallen ** - ft_spike_psth
‘yes’ (default) Accept variable trial lengths and use all available trials and the samples in every trial. Missing values will be ignored in the computation of the average and the variance and stored as NaNs in the output psth.trial. ‘no’ Only select those trials that fully cover the window as specified by cfg.latency and discard those trials that do not.

** cfg.vartriallen ** - ft_spikedensity
‘yes’ (default) or ‘no’. ‘yes’ - accept variable trial lengths and use all available trials and the samples in every trial. Missing values will be ignored in the computation of the average and the variance. ‘no’ - only select those trials that fully cover the window as specified by cfg.latency.

** cfg.vartriallen ** - ft_spike_rate
‘yes’ (default) or ‘no’. If ‘yes’ - accept variable trial lengths and use all available trials and the samples in every trial. If ‘no’ - only select those trials that fully cover the window as specified by cfg.latency and discard those trials that do not.

** cfg.vartriallen ** - ft_spike_xcorr
‘yes’ (default) or ‘no’. If ‘yes’ - accept variable trial lengths and use all available trials and the samples in every trial. If ‘no’ - only select those trials that fully cover the window as specified by cfg.latency and discard those trials that do not. if cfg.method = ‘yes’, then cfg.vartriallen should be ‘no’ (otherwise, fewer coincidences will occur because of non-overlapping windows)

** cfg.velocity2D.kernel ** - ft_detect_movement
vector 1 x nsamples, kernel to compute velocity (default = [1 1 0 -1 -1].*(data.fsample/6); cfg.velocity2D.demean = ‘no’ or ‘yes’, whether to apply centering correction (default = ‘yes’) cfg.velocity2D.mindur = minimum microsaccade durantion in samples (default = 3); cfg.velocity2D.velthres = threshold for velocity outlier detection (default = 6);

** cfg.verbose ** - ft_neighbourplot
string, ‘yes’ or ‘no’, whether the function will print feedback text in the command window

** cfg.vertexcolor ** - ft_sourceplot
[r g b] values or string, for example ‘brain’, ‘cortex’, ‘skin’, ‘black’, ‘red’, ‘r’, or an Nx3 or Nx1 array where N is the number of vertices

** cfg.verticalpadding ** - ft_databrowser
number or ‘auto’, padding to be added to top and bottom of plot to avoid channels largely dissappearing when viewmode = ‘vertical’/’component’ (default = ‘auto’). The padding is expressed as a proportion of the total height added to the top and bottom. The setting ‘auto’ determines the padding depending on the number of channels that are being plotted.

** cfg.videofile ** - ft_audiovideobrowser
string with the filename

** cfg.videohdr ** - ft_audiovideobrowser
header structure of the video data, see FT_READ_HEADER

** cfg.viewmode ** - ft_volumerealign
‘ortho’ or ‘surface’, visualize the anatomical MRI as three slices or visualize the extracted head surface (default = ‘ortho’)

** cfg.viewmode ** - ft_databrowser
string, ‘butterfly’, ‘vertical’, ‘component’ for visualizing ICA/PCA components (default is ‘butterfly’)

** cfg.viewpoint ** - ft_prepare_layout
string indicating the view point that is used for orthographic projection of 3-D sensor positions to the 2-D plane. The possible viewpoints are ‘left’ - left sagittal view, L=anterior, R=posterior, top=top, bottom=bottom ‘right’ - right sagittal view, L=posterior, R=anterior, top=top, bottom=bottom ‘inferior’ - inferior axial view, L=R, R=L, top=anterior, bottom=posterior ‘superior’ - superior axial view, L=L, R=R, top=anterior, bottom=posterior ‘anterior’ - anterior coronal view, L=R, R=L, top=top, bottom=bottom ‘posterior’ - posterior coronal view, L=L, R=R, top=top, bottom=bottom ‘auto’ - automatic guess of the most optimal of the above tip: use cfg.viewpoint = ‘auto’ per iEEG electrode grid/strip/depth for more accurate results tip: to obtain an overview of all iEEG electrodes, choose superior/inferior, use cfg.headshape/mri, and plot using FT_LAYOUTPLOT with cfg.box/mask = ‘no’

** cfg.viewresult ** - ft_volumerealign
string, ‘yes’ or ‘no’, whether or not to visualize aligned volume(s) after realignment (default = ‘no’)

** cfg.visible ** - ft_clusterplot
string, ‘on’ or ‘off’ whether figure will be visible (default = ‘on’)

** cfg.visible ** - ft_neighbourplot, ft_sourceplot
string, ‘on’ or ‘off’, whether figure will be visible (default = ‘on’)

** cfg.visible ** - ft_layoutplot
string, ‘yes’ or ‘no’ whether figure will be visible (default = ‘yes’)

** cfg.visualize ** - ft_qualitycheck
string, ‘yes’ or ‘no’ to visualize the analysis (default = ‘yes’)

** cfg.vmpversion ** - ft_volumewrite
1 or 2 (default) version of the vmp-format to use

W

** cfg.ward ** - ft_spikesorting
substructure with additional low-level options for this method

** cfg.ward.distance ** - ft_spikesorting
‘L1’, ‘L2’, ‘correlation’, ‘cosine’

** cfg.warp ** - ft_electroderealign
‘dykstra2012’, or ‘hermes2010’

** cfg.warp ** - ft_electroderealign
‘fsaverage’

** cfg.warp ** - ft_electroderealign
string describing the spatial transformation for the template and headshape methods ‘rigidbody’ apply a rigid-body warp (default) ‘globalrescale’ apply a rigid-body warp with global rescaling ‘traditional’ apply a rigid-body warp with individual axes rescaling ‘nonlin1’ apply a 1st order non-linear warp ‘nonlin2’ apply a 2nd order non-linear warp ‘nonlin3’ apply a 3rd order non-linear warp ‘nonlin4’ apply a 4th order non-linear warp ‘nonlin5’ apply a 5th order non-linear warp ‘dykstra2012’ non-linear wrap only for headshape method, useful for projecting ECoG onto cortex hull ‘fsaverage’ surface-based realignment with FreeSurfer fsaverage brain ‘fsinflated’ surface-based realignment with FreeSurfer individual subject inflated brain

** cfg.whichEcho ** - ft_omri_pipeline_nuisance
which echo to process for multi-echo sequences (default = 1)

** cfg.whitebg ** - ft_sliceinterp
‘yes’ or ‘no’ (default = ‘yes’)

** cfg.width ** - ft_freqanalysis, ft_freqanalysis
‘width’, or number of cycles, of the wavelet (default = 7)

** cfg.widthparam ** - ft_topoplotCC
string, parameter to be used to control the line width (see below)

** cfg.window ** - ft_spike_plot_isireturn
‘no’, ‘gausswin’ or ‘boxcar’ ‘gausswin’ is N-by-N multivariate gaussian, where the diagonal of the covariance matrix is set by cfg.gaussvar. ‘boxcar’ is N-by-N rectangular window.

** cfg.window ** - ft_spike_plot_jpsth
‘string’ or N-by-N matrix ‘no’: apply no smoothing ‘ gausswin’ use a Gaussian smooth function ‘ boxcar’ use a box-car to smooth

** cfg.winfunc ** - ft_spikedensity
(a) string or function handle, type of window to convolve with (def = ‘gauss’). - ‘gauss’ (default) - ‘alphawin’, given by win = x*exp(-x/timeconstant) - For standard window functions in the signal processing toolbox see WINDOW. (b) vector of length nSamples, used directly as window

** cfg.winfuncopt ** - ft_spikedensity
options that go with cfg.winfunc For cfg.winfunc = ‘alpha’: the timeconstant in seconds (default = 0.005s) For cfg.winfunc = ‘gauss’: the standard deviation in seconds (default = 1/4 of window duration in seconds) For cfg.winfunc = ‘wname’ with ‘wname’ any standard window function see window opts in that function and add as cell array If cfg.winfunctopt = [], default opts are taken.

** cfg.winlen ** - ft_spike_plot_jpsth
cfg.window length in seconds (default = 5binwidth). length of our window is 2round*(cfg.winlen/binwidth) where binwidth is the binwidth of the jpsth (jpsth.time(2)-jpsth.time(1)).

** cfg.winlen ** - ft_spike_plot_isireturn
window length in seconds (default = 5cfg.dt). The total length of our window is 2round*(cfg.winlen/cfg.dt) +1;

** cfg.winstepsize ** - ft_spiketriggeredspectrum_stat
double, stepsize of sliding window in seconds. For example if cfg.winstepsize = 0.1, we compute stat every other 100 ms.

** cfg.write ** - ft_volumenormalise
‘no’ (default) or ‘yes’, writes the segmented volumes to SPM2 compatible analyze-file, with the suffix _anatomy for the anatomical MRI volume _param for each of the functional volumes

** cfg.write ** - ft_volumesegment
‘no’ or ‘yes’ (default = ‘no’), writes the probabilistic tissue maps to SPM compatible analyze (spm2), or nifti (spm8/spm12) files, with the suffix (spm2) _seg1, for the gray matter segmentation _seg2, for the white matter segmentation _seg3, for the csf segmentation or with the prefix (spm8, and spm12 with spmmethod=’old’) c1, for the gray matter segmentation c2, for the white matter segmentation c3, for the csf segmentation when using spm12 with spmmethod=’new’ there’ll be 3 additional tissue types c4, for the bone segmentation c5, for the soft tissue segmentation c6, for the air segmentation when using spm12 with spmmethod=’mars’ the tpms will be postprocessed with the mars toolbox, yielding smoother% segmentations in general.

** cfg.wvar ** - ft_statistics_analytic
number or list with indices, within-block variable(s)

** cfg.wvar ** - ft_statistics_montecarlo
number or list with indices, within-cell variable(s)

X

** cfg.xlim ** - ft_movieplotER, ft_multiplotER, ft_multiplotTFR, ft_singleplotER, ft_singleplotTFR
‘maxmin’ or [xmin xmax] (default = ‘maxmin’)

** cfg.xlim ** - ft_realtime_headlocalizer
[min max], range in cm to plot (default = [-15 15])

** cfg.xlim ** - ft_topoplotER, ft_topoplotTFR
limit for 1st dimension in data (e.g., time), can be ‘maxmin’ or [xmin xmax] (default = ‘maxmin’)

** cfg.xlim ** - ft_connectivityplot
selection boundaries over first dimension in data (e.g., freq) ‘maxmin’ or [xmin xmax] (default = ‘maxmin’)

** cfg.xlim ** - ft_movieplotTFR
selection boundaries over first dimension in data (e.g., time) ‘maxmin’ or [xmin xmax] (default = ‘maxmin’)

** cfg.xrange ** - ft_volumereslice
[min max], in physical units

Y

** cfg.ylim ** - ft_multiplotTFR, ft_singleplotTFR
‘maxmin’ or [ymin ymax] (default = ‘maxmin’)

** cfg.ylim ** - ft_multiplotER, ft_singleplotER
‘maxmin’, ‘maxabs’, ‘zeromax’, ‘minzero’, or [ymin ymax] (default = ‘maxmin’)

** cfg.ylim ** - ft_spike_plot_isi
[min max] or ‘auto’ (default) If ‘auto’, we plot from 0 to 110% of maximum plotted value);

** cfg.ylim ** - ft_spike_plot_psth
[min max] or ‘auto’ (default) If ‘standard’, we plot from 0 to 110% of maximum plotted value);

** cfg.ylim ** - ft_realtime_headlocalizer
[min max], range in cm to plot (default = [-15 15])

** cfg.ylim ** - ft_topoplotTFR
limit for 2nd dimension in data (e.g., freq), can be ‘maxmin’ or [ymin ymax] (default = ‘maxmin’)

** cfg.ylim ** - ft_movieplotTFR
selection boundaries over second dimension in data (e.g., freq) ‘maxmin’ or [xmin xmax] (default = ‘maxmin’)

** cfg.ylim ** - ft_connectivityplot
selection boundaries over second dimension in data (i.e. ,time, if present), ‘maxmin’, or [ymin ymax] (default = ‘maxmin’)

** cfg.ylim ** - ft_databrowser
vertical scaling, can be ‘maxmin’, ‘maxabs’ or [ymin ymax] (default = ‘maxabs’)

** cfg.yrange ** - ft_volumereslice
[min max], in physical units

Z

** cfg.zlim ** - ft_realtime_headlocalizer
[min max], range in cm to plot (default is automatic)

** cfg.zlim ** - ft_databrowser
color scaling to apply to component topographies, ‘minmax’, ‘maxabs’ (default = ‘maxmin’)

** cfg.zlim ** - ft_topoplotER, ft_topoplotTFR
limits for color dimension, ‘maxmin’, ‘maxabs’, ‘zeromax’, ‘minzero’, or [zmin zmax] (default = ‘maxmin’)

** cfg.zlim ** - ft_connectivityplot
plotting limits for color dimension, ‘maxmin’, ‘maxabs’ or [zmin zmax] (default = ‘maxmin’)

** cfg.zlim ** - ft_movieplotER, ft_movieplotTFR, ft_multiplotTFR, ft_singleplotTFR, ft_topoplotIC
plotting limits for color dimension, ‘maxmin’, ‘maxabs’, ‘zeromax’, ‘minzero’, or [zmin zmax] (default = ‘maxmin’)

** cfg.zrange ** - ft_volumereslice
[min max], in physical units

** cfg.zscore ** - ft_mvaranalysis
‘no’ (default) or ‘yes’ specifies whether the channel data are z-transformed prior to the model fit. This may be necessary if the magnitude of the signals is very different e.g. when fitting a model to combined MEG/EMG data

** cfg.zscore ** - ft_denoise_pca
standardise reference data prior to PCA (default = ‘no’)

** cfg.zthresh.mindist ** - ft_spikedetection
mininum distance in samples between detected peaks

** cfg.zthresh.neg ** - ft_spikedetection
negative threshold, e.g. -3

** cfg.zthresh.offset ** - ft_spikedetection
number of samples before peak (default = 16)

** cfg.zthresh.pos ** - ft_spikedetection
positive threshold, e.g. 3