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 1.
Default: 1
- -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 beggining 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