roisummarize

Description:

Inputs:

Outputs:

Usage:

Extract summary timecourses from the regions in an atlas

usage: roisummarize [-h] [--samplerate FREQ | --sampletstep TSTEP]
                    [--numskip NPTS]
                    [--filterband {None,vlf,lfo,resp,cardiac,hrv_ulf,hrv_vlf,hrv_lf,hrv_hf,hrv_vhf,lfo_legacy}]
                    [--filterfreqs LOWERPASS UPPERPASS]
                    [--filterstopfreqs LOWERSTOP UPPERSTOP]
                    [--normmethod {None,percent,variance,stddev,z,p2p,mad}]
                    [--debug]
                    inputfilename templatefile outputfile

Positional Arguments

inputfilename

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

templatefile

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

outputfile

Name of the output text file.

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

--numskip

Skip NPTS initial points to get past T1 relaxation.

Default: 0

--debug

Enable additional debugging output.

Default: False

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 “None”.

Default: “None”

--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.

Normalization options

--normmethod

Possible choices: None, percent, variance, stddev, z, p2p, mad

Demean and normalize timecourses using one of the following methods: “None” - demean only; “percent” - divide by mean; “variance” - divide by variance; “stddev” or “z” - divide by standard deviation; “p2p” - divide by range; “mad” - divide by median absolute deviation. Default is “None”.

Default: “None”