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}]
[--filterfreqs LOWERPASS UPPERPASS]
[--filterstopfreqs LOWERSTOP UPPERSTOP]
[--filtertype {trapezoidal,brickwall,butterworth}]
[--butterorder ORDER] [--padseconds SECONDS]
[--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
Filter data and regressors to specific band. Use “None” to disable filtering. Default is “lfo”.
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 filtered timecourse to reduce end effects. Default is 30.0.
Default: 30.0
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