Command-line usage

You can invoke the primary workflow of phys2bids from the command line.

The phys2bids command

usage: phys2bids [-h] -in FILENAME [-info] [-indir INDIR] [-outdir OUTDIR]
                 [-heur HEUR_FILE] [-sub SUB] [-ses SES] [-chtrig CHTRIG]
                 [-chsel [CHSEL [CHSEL ...]]]
                 [-ntp [NUM_TIMEPOINTS_EXPECTED [NUM_TIMEPOINTS_EXPECTED ...]]]
                 [-tr [TR [TR ...]]] [-thr THR] [-pad PAD]
                 [-chnames [CH_NAME [CH_NAME ...]]] [-yml YML] [-debug]
                 [-quiet] [-v]

Required Argument:

-in, --input-file

The name of the file containing physiological data, with or without extension.

Named Arguments

-info, --info

Only output info about the file, don’t process. Default is to process.

Default: False

-indir, --input-dir

Folder containing input. Default is current folder.

Default: “.”

-outdir, --output-dir

Folder where output should be placed. Default is current folder. If “-heur” is used, it’ll become the site folder. Requires “-sub”. Optional to specify “-ses”.

Default: “.”

-heur, --heuristic

File containing heuristic, with or without extension. This file is needed in order to convert your input file to BIDS format! If no path is specified, it assumes the file is in the current folder. Edit the heur_ex.py file in heuristics folder.

-sub, --subject

Specify alongside “-heur”. Code of subject to process.

-ses, --session

Specify alongside “-heur”. Code of session to process.

-chtrig, --channel-trigger

The column number of the trigger channel. Channel numbering starts with 1. Default is 0. If chtrig is left as zero phys2bids will perform an automatic trigger channel search by channel names.

Default: 0

-chsel, --channel-selection

The column numbers of the channels to process. Default is to process all channels.

-ntp, --numtps

Number of expected trigger timepoints (TRs). Default is None. Note: the estimation of beginning of neuroimaging acquisition cannot take place with this default. If you’re running phys2bids on a multi-run recording, give a list of each expected ntp for each run.

-tr, --tr

TR of sequence in seconds. If you’re running phys2bids on a multi-run recording, you can give a list of each expected ntp for each run, or just one TR if it is consistent throughout the session.

-thr, --threshold

Threshold to use for trigger detection. If “ntp” and “TR” are specified, phys2bids automatically computes a threshold to detect the triggers. Use this parameter to set it manually. This parameter is necessary for multi-run recordings.

-pad, --padding

Padding in seconds used around a single run when separating multi-run session files. Default is 9 seconds.

Default: 9

-chnames, --channel-names

Column header (for json file output).

Default: []

-yml, --participant-yml

full path to file with info needed to generate participant.tsv file

Default: “”

-debug, --debug

Only print debugging info to log file. Default is False.

Default: False

-quiet, --quiet

Only print warnings to log file. Default is False.

Default: False

-v, --version

show program’s version number and exit