localflow

Description:

Inputs:

Outputs:

Usage:

Calculate local sources of signal.

usage: localflow [-h] [--npasses NPASSES] [--radius RADIUS]
                 [--minlagdiff MINLAGDIFF] [--ampthresh AMPTHRESH]
                 [--gausssigma GAUSSSIGMA] [--oversampfac OVERSAMPFAC]
                 [--dofit] [--detrendorder ORDER] [--nosphere]
                 [--filterband {None,vlf,lfo,resp,cardiac,hrv_ulf,hrv_vlf,hrv_lf,hrv_hf,hrv_vhf,lfo_legacy,lfo_tight}]
                 [--filterfreqs LOWERPASS UPPERPASS]
                 [--filterstopfreqs LOWERSTOP UPPERSTOP]
                 [--filtertype {trapezoidal,brickwall,butterworth}]
                 [--butterorder ORDER] [--padseconds SECONDS]
                 [--padtype {reflect,zero,cyclic,constant,constant+}]
                 [--windowfunc {hamming,hann,blackmanharris,None}]
                 [--zeropadding PADVAL] [--noprogressbar] [--debug]
                 inputfilename outputroot

Positional Arguments

inputfilename

The name of the input nifti file.

outputroot

The root name of the output nifti files.

Named Arguments

--npasses

The number of passes for reconstruction. Default is 20

Default: 20

--radius

The radius around the voxel to check correlations. Default is 10.5

Default: 10.5

--minlagdiff

The minimum lagtime difference threshold to select which diffs to include in reconstruction. Default is 0.0

Default: 0.0

--ampthresh

The correlation threshold to select which diffs to include in reconstruction. Default is 0.3

Default: 0.3

--gausssigma

Spatially filter fMRI data prior to analysis using GAUSSSIGMA in mm. Set GAUSSSIGMA negative to set it to half the mean voxel dimension (a rule of thumb for a good value).

Default: 0.0

--oversampfac

Oversample the fMRI data by the following integral factor. Set to -1 for automatic selection (default).

Default: -1

--dofit

Turn on correlation fitting.

Default: False

--detrendorder

Set order of trend removal (0 to disable). Default is 3.

Default: 3

--nosphere

Use rectangular rather than spherical reconstruction kernel.

Default: True

Filtering options

--filterband

Possible choices: None, vlf, lfo, resp, cardiac, hrv_ulf, hrv_vlf, hrv_lf, hrv_hf, hrv_vhf, lfo_legacy, lfo_tight

Filter data and regressors to specific band. Use “None” to disable filtering. Default is “lfo”. Ranges are: vlf: 0.0-0.009Hz, lfo: 0.01-0.15Hz, cardiac: 0.66-3.0Hz, hrv_ulf: 0.0-0.0033Hz, hrv_vlf: 0.0033-0.04Hz, hrv_lf: 0.04-0.15Hz, hrv_hf: 0.15-0.4Hz, hrv_vhf: 0.4-0.5Hz, lfo_legacy: 0.01-0.15Hz, lfo_tight: 0.01-0.1Hz

Default: 'lfo'

--filterfreqs

Filter data and regressors to retain LOWERPASS to UPPERPASS. If –filterstopfreqs is not also specified, LOWERSTOP and UPPERSTOP will be calculated automatically.

--filterstopfreqs

Filter data and regressors to with stop frequencies LOWERSTOP and UPPERSTOP. LOWERSTOP must be <= LOWERPASS, UPPERSTOP must be >= UPPERPASS. Using this argument requires the use of –filterfreqs.

--filtertype

Possible choices: trapezoidal, brickwall, butterworth

Filter data and regressors using a trapezoidal FFT, brickwall FFT, or butterworth bandpass filter. Default is “trapezoidal”.

Default: 'trapezoidal'

--butterorder

Set order of butterworth filter (if used). Default is 6.

Default: 6

--padseconds

The number of seconds of padding to add to each end of a timecourse to be filtered to reduce end effects. Default is 30.0.

Default: 30.0

--padtype

Possible choices: reflect, zero, cyclic, constant, constant+

The type of padding at each end of a timecourse to be filtered to reduce end effects. Default is “reflect”.

Default: 'reflect'

Windowing options

--windowfunc

Possible choices: hamming, hann, blackmanharris, None

Window function to use prior to correlation. Options are hamming, hann, blackmanharris, and None. Default is hamming

Default: 'hamming'

--zeropadding

Pad input functions to correlation with PADVAL zeros on each side. A PADVAL of 0 does circular correlations, positive values reduce edge artifacts. Set PADVAL < 0 to set automatically. Default is 0.

Default: 0

Miscellaneous options

--noprogressbar

Will disable showing progress bars (helpful if stdout is going to a file).

Default: True

--debug

Turn on debugging information.

Default: False