ccorrica

Description:

Find temporal crosscorrelations between the columns of an input file

Inputs:

A text file containing one or more timeseries columns. Use [:COLSPEC] to select which column(s) to use, where COLSPEC is an integer, a column separated list of ranges, or a comma separated set of column names (if input file is BIDS). Default is to use all columns.

Outputs:

Various NIFTI and text files with the correlation information.

Usage:

Find temporal crosscorrelations between a set of timecourses

usage: ccorrica [-h] [--samplerate FREQ | --sampletstep TSTEP]
                [--windowfunc {hamming,hann,blackmanharris,None}]
                [--zeropadding PADVAL] [--searchrange LAGMIN LAGMAX]
                [--filterband {None,vlf,lfo,resp,cardiac,hrv_ulf,hrv_vlf,hrv_lf,hrv_hf,hrv_vhf,lfo_legacy}]
                [--filterfreqs LOWERPASS UPPERPASS]
                [--filterstopfreqs LOWERSTOP UPPERSTOP]
                [--corrweighting {None,phat,liang,eckart}]
                [--detrendorder DETRENDORDER]
                [--oversampfactor OVERSAMPFACTOR] [--debug]
                timecoursefile outputroot

Positional Arguments

timecoursefile

Text file containing one or more timeseries columns. Use [:COLSPEC] to select which column(s) to use, where COLSPEC is an integer, a column separated list of ranges, or a comma separated set of column names (if input file is BIDS). Default is to use all columns

outputroot

Root name for the output files

Named Arguments

--samplerate

Timecourses in file have sample frequency FREQ (default is 1.0Hz) NB: –samplerate and –sampletstep) are two ways to specify the same thing.

Default: auto

--sampletstep

Timecourses in file have sample timestep TSTEP (default is 1.0s) NB: –samplerate and –sampletstep) are two ways to specify the same thing.

Default: auto

--searchrange

Limit fit to a range of lags from LAGMIN to LAGMAX. Default is -30.0 to 30.0 seconds.

Default: (-30.0, 30.0)

--corrweighting

Possible choices: None, phat, liang, eckart

Method to use for cross-correlation weighting. Default is None.

Default: “None”

--detrendorder

Detrending order (default is 1 - linear). Set to 0 to disable

Default: 1

--oversampfactor

Factor by which to oversample timecourses prior to correlation. Default is 1. If set negative, factor will be set automatically.

Default: 1

--debug

Enable additional debugging output.

Default: False

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

Filtering options

--filterband

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

Filter timecourses to specific band. Use “None” to disable filtering. Default is “lfo”.

Default: “lfo”

--filterfreqs

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

--filterstopfreqs

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