Index of configuration options

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

This index to the reference documentation is automatically generated from the MATLAB code every day. Therefore you should not edit this page manually, since your changes would be overwritten automatically. If you want to suggest corrections to the documentation, please send them by email to the mailing list or to one of the main developers (see contact).

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.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.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 'auto').

cfg.appenddim ft_appendtimelock
String. The dimension to concatenate over (default: 'auto'). 'chan' and 'rpt' possible (even if averaged data)

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) (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.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.reject ft_rejectartifact
'none', 'partial','nan', or 'complete' (default = 'complete')

cfg.artfctdef.threshold.bpfilter ft_artifact_threshold
'no' or '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/T, default inf

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

cfg.artfctdef.threshold.range ft_artifact_threshold
value in uV/T, default inf

cfg.artfctdef.tms.artpadding ft_artifact_tms
0.01 (Be aware that if one artifact falls within this specified range of another artifact, both artifact will be counted as one. Depending on cfg.prestim and cfg.poststim you may not mark enough data as artifactual.)

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.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 should 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 in “ortho-plotting” mode (see “ortho-plotting” below)

cfg.atlas ft_volumelookup
string, filename of atlas to use, either the AFNI brik file that is available from http://afni.nimh.nih.gov/afni/doc/misc/afni_ttatlas/, or the WFU atlasses available from http://fmri.wfubmc.edu. see FT_READ_ATLAS

cfg.atlas ft_volumelookup
string, filename of atlas to use, either the AFNI brik file that is available from http://afni.nimh.nih.gov/afni/doc/misc/ttatlas_tlrc, or the WFU atlasses available from http://fmri.wfubmc.edu. 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_freqstatistics, ft_timelockstatistics
'yes' or 'no' (default = 'no')

cfg.avgoverfreq ft_freqstatistics
'yes' or 'no' (default = 'no')

cfg.avgovertime ft_freqstatistics, ft_timelockstatistics
'yes' or 'no' (default = 'no')

cfg.axes ft_multiplotER
'yes', 'no' (default = 'yes') Draw x- and y-axes for each graph

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
'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_singleplotTFR
'yes','no' or [time1 time2] (default = 'no'), see FT_FREQBASELINE

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_singleplotER
'yes','no' or [time1 time2] (default = 'no'), see ft_timelockbaseline

cfg.baseline ft_prepare_headmodel
(optional)

cfg.baseline ft_freqbaseline, ft_timelockbaseline
[begin end] (default = 'no')

cfg.baseline ft_timelocksimulation
number (default = 0.3)

cfg.baselinetype ft_movieplotER, ft_movieplotTFR, ft_multiplotER, 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
[begin end] in seconds, the default is the complete trial (default = 'all')

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.blocksize ft_databrowser
duration in seconds for cutting the data up

cfg.bootstrap ft_sourceanalysis
'no' or 'yes' bootstrap resampling of trials

cfg.box ft_multiplotTFR
'yes', 'no' (default = 'no' if maskparameter given default = 'yes') Draw a box around each graph

cfg.box ft_multiplotER
'yes', 'no' (default = 'no') 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.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 [low high] in Hz

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

cfg.bsinstabilityfix ft_preprocessing
deal with filter instability, 'no', 'reduce', 'split' (default = 'no')

cfg.bw ft_prepare_layout
if an image is used and bw = 1 transforms the image in black and white (default = 0, do not transform)

C

cfg.camlight ft_sourceplot
'yes' or 'no' (default = 'yes')

cfg.casesensitive ft_electroderealign, ft_sensorrealign
'yes' or 'no', determines whether string comparisons between electrode labels are case sensitive (default = 'yes')

cfg.chanhigh ft_crossfrequencyanalysis
selection of channels for the high frequency, see FT_CHANNELSELECTION

cfg.chanlow ft_crossfrequencyanalysis
selection of channels for the low frequency, see FT_CHANNELSELECTION

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_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_electrodeplacement
Nx1 cell-array with selection of channels (default = '1','2', …)

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

cfg.channel ft_appendtimelock, 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_sensorrealign, ft_singleplotTFR, ft_sourceanalysis, 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_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
cell-array with channel selection (default = 'all'), see FT_CHANNELSELECTION for details

cfg.channel ft_timelockbaseline
cell-array, see FT_CHANNELSELECTION

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_denoise_pca
the channels to be denoised (default = 'MEG')

cfg.channelcmb ft_freqanalysis
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_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.chanscale ft_databrowser
Nx1 vector with scaling factors, one per channel specified in cfg.channel

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.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.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.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.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_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.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_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.combinegrad ft_combineplanar
'yes'

cfg.comment ft_annotate
string

cfg.comment ft_topoplotTFR
string 'no' 'auto' or 'xlim' (default = 'auto') 'auto': date, xparam and parameter limits are printed 'xlim': only xparam limits are printed

cfg.comment ft_topoplotER, 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
string of text (default = date + colors) Add 'comment' to graph (according to COMNT in the layout)

cfg.comment ft_multiplotTFR
string of text (default = date + zlimits) 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_zvalue

cfg.continuous ft_databrowser
'yes' or 'no' whether the data should be interpreted as continuous or trial-based

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
'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.coordsys ft_volumewrite
'spm' or 'ctf', this will only affect the functionality in case filetype = 'analyze', 'vmp', or 'vmr'

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', 'spm', 'tal' and 'paxinos'. See http://tinyurl.com/ojkuhqz

cfg.coordsys ft_preprocessing
string, 'head' or 'dewar' (default = 'head')

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.covariance ft_timelockanalysis
'no' or 'yes' (default = 'no')

cfg.covariancewindow ft_timelockanalysis
'prestim', 'poststim', 'all' or [begin end] (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_artifact_ecg

cfg.datafile ft_artifact_clip, 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_zvalue

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

cfg.dataset ft_artifact_ecg

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_artifact_clip, 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.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.demean ft_resampledata
'no' or 'yes', baseline correct the data prior to resampling (default = 'no')

cfg.demean ft_preprocessing
'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.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.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.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_multiplotER, 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.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_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.dss.denf.function ft_componentanalysis

cfg.dss.denf.params ft_componentanalysis

E

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

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_sensorrealign, 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_sensorrealign, 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.enableedit ft_neighbourplot
'yes' or 'no' (default). allows the user to flexibly add or remove edges between vertices

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

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

cfg.equalbinavg ft_stratify
'yes'

cfg.eta ft_sourcedescriptives
'yes' or 'no' (default = 'no')

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.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_resampledata, ft_sourceanalysis
'no', 'text', 'textbar', 'gui' (default = 'text')

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_electroderealign, ft_prepare_neighbours, ft_sensorrealign
'yes' or 'no' (default = 'no')

cfg.feedback ft_electroderealign
'yes' or 'no' (feedback includes the output 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_connectivityanalysis
string, specifying the feedback presented to the user. Default is 'none'. See FT_PROGRESS

cfg.fiducial ft_electroderealign, ft_sensorrealign
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.lpa ft_volumerealign
[i j k], position of LPA

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

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

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

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

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

cfg.fiducial.rpa ft_volumewrite
[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.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.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, 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_freqanalysis, ft_freqanalysis
[begin end], frequency band of interest

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, 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.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_dipolefitting, ft_sourceanalysis
single number (in Hz)

cfg.fsample ft_connectivitysimulation
in Hz

cfg.fsample ft_dipolesimulation
sampling frequency in Hz

cfg.fsample ft_freqsimulation
simulated sample frequency

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

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.ftest ft_regressconfound
string array, {N X Nconfounds}, to F-test whether the full model explains more variance than reduced models (e.g. {'1 2'; '3 4'; '5'} where iteratively the added value of regressors 1 and 2, and then 3 and 4, etc., are tested)

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 = 'pow')

G

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_sensorrealign, 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_sensorrealign, 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_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.dim ft_dipolefitting, ft_prepare_leadfield, ft_prepare_sourcemodel, ft_sourceanalysis
[Nx Ny Nz] vector with dimensions in case of 3-D 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.headerfile ft_artifact_ecg

cfg.headerfile ft_artifact_clip, 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_zvalue

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.headshape ft_prepare_mesh
'/path/to/surf/lh.pial'; cortex_hull = ft_prepare_mesh(cfg);

cfg.headshape ft_prepare_mesh
(optional) 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, ft_sensorrealign
a filename containing headshape, a structure containing a single triangulated boundary, or a Nx3 matrix with surface points

cfg.headshape ft_prepare_mesh
a filename containing the pial surface computed by freesurfer recon-all ('/path/to/surf/lh.pial')

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_prepare_sourcemodel
string, should be a *.fif file

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_topoplotIC, ft_topoplotTFR
'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
1×5 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
1×5 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
1×5 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.hlim ft_multiplotER
'maxmin' or [xmin xmax] (default = 'maxmin')

cfg.hotkeys ft_multiplotTFR, ft_singleplotTFR, ft_topoplotER, ft_topoplotTFR
enables hotkeys (up/down arrows) for dynamic colorbar adjustment

cfg.hotkeys ft_singleplotER
enables hotkeys (up/down/left/right arrows) for dynamic x/y axis translation (Ctrl+) and zoom 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.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
'edge', 'surface' or 'both' (default = 'edge')

cfg.individual.headshape ft_interactiverealign
structure, see FT_READ_HEADSHAPE

cfg.individual.headshapestyle ft_interactiverealign
'vertex', 'surface' or 'both' (default = 'vertex')

cfg.inputcoord ft_volumelookup, ft_volumelookup
'mni' or 'tal', coordinate system of the mri/source/stat

cfg.inputfile ft_analysispipeline, ft_annotate, ft_anonimizedata, ft_appenddata, ft_appendfreq, ft_artifact_clip, ft_artifact_ecg, ft_artifact_eog, ft_artifact_jump, ft_artifact_muscle, ft_artifact_threshold, ft_artifact_tms, ft_channelnormalise, ft_channelrepair, ft_clusterplot, ft_combineplanar, ft_componentanalysis, ft_connectivityanalysis, ft_crossfrequencyanalysis, 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_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_audiovideobrowser
'yes' or 'no' (default = 'yes')

cfg.interactive ft_sliceinterp
'yes' or 'no' (default), interactive coordinates and source values

cfg.interactive ft_multiplotER, 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.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.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.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')

K

cfg.keepbrain ft_defacevolume
'no' or 'yes', segment and retain the brain (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_anonimizedata
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_anonimizedata
'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.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_freqdescriptives
'yes' or 'no', estimate single trial power (useful for fourier data) (default = 'no')

cfg.keeptrials ft_freqanalysis, 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_anonimizedata
cell-array with strings, values to keep (default = {})

cfg.kurtosis ft_sourcedescriptives
'yes' or 'no' (default = 'no')

L

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_dipolefitting, ft_freqstatistics, ft_timelockgrandaverage, ft_timelockstatistics
[begin end] in seconds or 'all' (default = 'all')

cfg.latency ft_rejectvisual
[begin end] in seconds, or 'minperlength', 'maxperlength', 'prestim', 'poststim' (default = 'maxperlength')

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

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_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_layoutplot
filename containg the layout

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

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.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_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_removetmsartifact
lowpass filter order

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

cfg.lpfilttype ft_removetmsartifact
digital filter type, 'but' or 'fir' or 'firls' (default = 'but')

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.lpfreq ft_removetmsartifact
number 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 = 2)

cfg.magscale 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 '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
[1×3] 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.maskalpha ft_multiplotTFR, ft_singleplotTFR
alpha value between 0 (transparant) and 1 (opaque) used for masking areas dictated by cfg.maskparameter (default = 1)

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_singleplotTFR
field in the data 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_topoplotER, ft_topoplotTFR
field in the data to be used for masking of data. Values between 0 and 1, 0 = transparent

cfg.maskparameter ft_multiplotTFR
field in the data to be used for opacity masking of data

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 lookedup, data in field should be logical

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

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

cfg.maskstyle ft_singleplotTFR
style used to masking, 'opacity', 'saturation' or 'outline' (default = 'opacity') use 'saturation' or 'outline' when saving to vector-format (like *.eps) to avoid all sorts of image-problems

cfg.maskstyle ft_multiplotTFR
style used to masking, 'opacity', 'saturation' or 'outline' (default = 'opacity') use 'saturation' or 'outline' when saving to vector-format (like *.eps) to avoid all sorts of image-problems (currently only possible with a white backgroud)

cfg.match ft_recodeevent
'exact' or 'nearest'

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

cfg.maxqueryrange ft_volumelookup
number, should be 1, 3, 5 (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.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_prepare_mesh
'cortexhull';

cfg.method ft_artifact_tms
'detect', TMS-artifacts are detected by preprocessing the data to be sensitive to transient high gradients, typical for TMS-pulses. 'marker', TMS-artifact onset and offsets are based on 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
'headshape'

cfg.method ft_stratify
'histogram' 'splithilo' 'splitlohi' 'splitlolo' 'splithihi' 'equatespike'

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_freqinterpolate
'nan', 'linear' (default = 'nan')

cfg.method ft_crossfrequencyanalysis
'plv' - phase locking value 'mvl' - mean vector length 'mi' - modulation index

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

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_channelrepair
'weighted', 'average', 'spline' or 'slap' (default = 'weighted')

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_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_sensorrealign
string representing the method for aligning or placing the electrodes 'fiducial' realign using three fiducials (e.g. NAS, LPA and RPA) 'template' realign the sensors to match a template set 'interactive' realign manually using a graphical user interface 'manual' manual positioning of the electrodes by clicking in a graphical user interface 'headshape' realign the sensors to fit the head surface

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

cfg.method ft_electrodeplacement
string representing the method for aligning or placing the electrodes 'mri' place electrodes in a brain volume 'headshape' place electrodes on the head surface

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

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_prepare_mesh
string, can be 'interactive', 'projectmesh', 'iso2mesh', 'isosurface', 'headshape', 'hexahedral', 'tetrahedral', 'cortexhull'

cfg.method ft_connectivitysimulation
string, can be 'linear_mix', 'mvnrnd', 'ar' (see below)

cfg.method ft_removetmsartifact
string, can be 'twopassfilter', 'interpolatepulse'

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_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.methods ft_globalmeanfield
string, whether the amplitude or power should be calculated (see below, default is 'amplitude')

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.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.model ft_regressconfound
string, 'yes' or 'no', whether to add the model to the output (default = 'no')

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.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.mva ft_statistics_crossvalidate
a multivariate analysis (default = {dml.standardizer dml.svm})

cfg.mvarmethod ft_mvaranalysis
scalar (only required when cfg.toolbox = '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.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.normalize ft_sourceanalysis
'no' or 'yes' (default = 'no')

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.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.ntrials ft_dipolesimulation
number of trials

cfg.ntrials ft_connectivitysimulation
scalar, number of trials

cfg.numbin ft_stratify
10

cfg.numbootstrap ft_sourceanalysis
number of bootstrap replications (e.g. number of original trials)

cfg.numclusters ft_headmovement
number of segments with constant headposition in which to split the data (default = 12)

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_redefinetrial
single number or Nx1 vector, expressed in samples relative to current t=0

cfg.offset ft_removetmsartifact
value, offset with respect to pulse onset to start filtering, in seconds.

cfg.offset ft_removetmsartifact
value, offset with respect to pulse onset to start replacing, in seconds.

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 possitive 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.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.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.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_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_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_anonimizedata, ft_appenddata, ft_appendfreq, ft_channelnormalise, ft_channelrepair, ft_combineplanar, ft_componentanalysis, ft_connectivityanalysis, ft_crossfrequencyanalysis, 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_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.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 layout is constructed from a sensor configuration structure (can be 'shift' (shift the positions in 2D space to remove the overlap (default)), 'keep' (don't shift, retain the overlap), 'no' (throw 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.parameter ft_volumerealign
'anatomy' the parameter which is used for the visualization

cfg.parameter ft_appendfreq
String. Specifies the name of the field to concatenate. For example, to concatenate freq1.powspctrm, freq2.powspctrm etc, use cft.parameter = 'powspctrm'.

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 'avg', 'powspctrm' or 'cohspctrm' (default depends on data.dimord)

cfg.parameter ft_multiplotER, ft_singleplotER
field to be plotted on y-axis (default depends on data.dimord) 'avg', 'powspctrm' or 'cohspctrm'

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.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.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.plotfiltresp ft_preprocessing
'no' or 'yes', plot filter responses (firws, default = 'no')

cfg.plotlabels ft_databrowser
'yes' (default), 'no', 'some'; whether to plot channel labels in vertical viewmode ('some' plots one in every ten labels; useful when plotting a large number of channels at a time)

cfg.plotunit ft_qualitycheck
scalar, the length of time to be plotted in one panel (default = 3600)

cfg.point ft_prepare_headmodel

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.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_databrowser
[begin end] in seconds, the default is the complete trial (default = 'all')

cfg.preproc.boxcar ft_rejectvisual
0.2

cfg.preproc.bpfilter ft_rejectvisual, ft_rejectvisual
'yes'

cfg.preproc.bpfiltord ft_rejectvisual
4

cfg.preproc.bpfiltord ft_rejectvisual
8

cfg.preproc.bpfilttype ft_rejectvisual, ft_rejectvisual
'but'

cfg.preproc.bpfreq ft_rejectvisual
[1 15]

cfg.preproc.bpfreq ft_rejectvisual
[110 140]

cfg.preproc.demean ft_databrowser
'no' or 'yes', whether to apply baseline correction (default = 'no')

cfg.preproc.detrend ft_databrowser
'no' or 'yes', remove linear trend from the data (done per trial) (default = 'no')

cfg.preproc.lpfilter ft_databrowser
'no' or 'yes' lowpass filter (default = 'no')

cfg.preproc.lpfreq ft_databrowser
lowpass frequency in Hz

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', 'gnomic' or 'inverse' (default = 'polar')

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.pulseonset ft_removetmsartifact
value or vector, time in seconds of the TMS pulse in seconds

cfg.pulsewidth ft_removetmsartifact
value, pulse pulsewidth to be removed in seconds

cfg.pulsewidth ft_removetmsartifact
value, pulse pulsewidth to be removed in seconds. If set to 0, entire trial will be filtered.

Q

cfg.queryrange ft_sourceplot
number, in atlas voxels (default 3)

R

cfg.radius ft_prepare_headmodel
(optional)

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.refchannel 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.refdip ft_sourceanalysis
reference dipole location (for coherence)

cfg.refmethod ft_preprocessing
'avg' or 'median' (default = 'avg')

cfg.reject ft_regressconfound
vector, [1 X Nconfounds], listing the confounds that are to be rejected (default = 'all')

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_anonimizedata
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_anonimizedata
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
'painters', 'zbuffer', ' opengl' or 'none' (default = [])

cfg.renderer ft_singleplotER, ft_singleplotTFR
'painters', 'zbuffer',' opengl' or 'none' (default = [])

cfg.renderer ft_databrowser
string, 'opengl', 'zbuffer', 'painters', see MATLAB Figure Properties. If the databrowser crashes, set to '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
Nx3 vector, coordinates of the points of interest

cfg.roi ft_volumelookup
string or cell of strings, region(s) of interest from anatomical atlas

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.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.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.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.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 which is evaluated using the right-click context menu The selected data and cfg.selcfg are passed on to this function.

cfg.shading ft_topoplotER, ft_topoplotIC, ft_topoplotTFR
'flat' 'interp' (default = 'flat')

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, ft_multiplotTFR
'yes', 'no' (default = 'no')

cfg.showoutline ft_multiplotER, ft_multiplotTFR
'yes', 'no' (default = 'no')

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.slicedim ft_sourceplot
dimension to slice 1 (x-axis) 2(y-axis) 3(z-axis) (default = 3)

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.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.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 256×256 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.spmversion ft_volumedownsample, ft_volumenormalise, ft_volumesegment
string, 'spm2' or 'spm8' (default = 'spm8')

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'

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.statistics ft_regressconfound
string, 'yes' or 'no', whether to add the statistics on the regression weights to the output (default = 'no')

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.t_ftimwin ft_freqanalysis
vector 1 x numfoi, length of time window (in seconds)

cfg.tail ft_statistics_analytic, ft_statistics_montecarlo, ft_statistics_stats
number, -1, 1 or 0 (default = 0)

cfg.taper ft_freqanalysis, 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.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_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.target ft_sensorrealign
list of electrode or gradiometer sets that are averaged into the standard

cfg.target ft_electroderealign
list of electrode sets that will be averaged

cfg.target ft_sensorrealign
single electrode or gradiometer set that serves as standard

cfg.target ft_electroderealign
single electrode set that serves as standard

cfg.target.label ft_electroderealign, ft_sensorrealign
{'NAS', 'LPA', 'RPA'}

cfg.target.pos ft_electroderealign, ft_sensorrealign
[0 -90 0] % location of the right ear

cfg.target.pos ft_electroderealign, ft_sensorrealign
[0 90 0] % location of the left ear

cfg.target.pos ft_electroderealign, ft_sensorrealign
[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.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
'edge', 'surface' or 'both' (default = 'edge')

cfg.template.headshape ft_interactiverealign
structure, see FT_READ_HEADSHAPE

cfg.template.headshapestyle ft_interactiverealign
'vertex', 'surface' or 'both' (default = 'vertex')

cfg.threshold ft_prepare_sourcemodel
0.1, relative to the maximum value in the segmentation

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.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_sourceplot
string, title of the figure window

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.toi ft_freqanalysis
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.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

cfg.tolerance ft_appendfreq
Double. Tolerance determines how different the units of frequency structures are allowed to be to be considered compatible (default: 1e-5).

cfg.toolbox 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.topolabel ft_componentanalysis
Nx1 cell-array with the channel labels

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.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.triallength ft_connectivitysimulation
in seconds

cfg.triallength ft_dipolesimulation
time in seconds

cfg.trials ft_channelnormalise, ft_channelrepair, ft_componentanalysis, ft_denoise_synthetic, ft_detect_movement, ft_freqanalysis, ft_freqdescriptives, ft_megplanar, ft_multiplotER, ft_multiplotTFR, 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_pca
list of trials that are used (default = 'all')

cfg.trl ft_artifact_zvalue

cfg.trl ft_headmovement, 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_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
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.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_componentanalysis, ft_rejectcomponent
'no' or 'yes' (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.vartrllength ft_timelockanalysis
0, 1 or 2 (see below)

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
'yes' or 'no', if 'yes' then the plot callback will include text output

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') padding is expressed as a proportion of the total height added to the top, and bottom) ('auto' adds padding depending on the number of channels 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 components e.g. from an ICA (default is 'butterfly')

cfg.viewresult ft_volumerealign
string, 'yes' or 'no', whether or not to visualize aligned volume(s) after realignment (default = 'no')

cfg.visualize ft_qualitycheck
string, 'yes' or 'no' to visualize the analysis (default = 'yes')

cfg.vlim ft_multiplotER
'maxmin', 'maxabs', 'zeromax', 'minzero', or [ymin ymax] (default = 'maxmin')

cfg.vmpversion ft_volumewrite
1 or 2 (default) version of the vmp-format to use

W

cfg.warp ft_electroderealign
'dykstra2012'

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.

cfg.warp ft_sensorrealign
string describing the spatial transformation for the template method '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

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.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) 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) c1, for the gray matter segmentation c2, for the white matter segmentation c3, for the csf segmentation

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_multiplotTFR, ft_singleplotER, ft_singleplotTFR
'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, ft_topoplotER, ft_topoplotTFR
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_singleplotER
'maxmin', 'maxabs', 'zeromax', 'minzero', or [ymin ymax] (default = 'maxmin')

cfg.ylim ft_movieplotTFR, ft_topoplotER
selection boundaries over second dimension in data (e.g., freq) 'maxmin' or [xmin xmax] (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_databrowser
color scaling to apply to component topographies, 'minmax', 'maxabs' (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_topoplotER, ft_topoplotIC, ft_topoplotTFR
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')

reference/index.txt · Last modified: 2016/08/17 23:02 (external edit)

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