fScan Reference Manual, Chapter 2 (CmdLineOptions): pysio
usage: -physio data flag [OPTNAME val OPTNAME2 val2 …]
PHYSIO analyzes analog physiological waveform data to extract parameters that can be used to correlate with other behavioral or imaging data.
The input DATA is assumed to be a series of time/amplitude values. DATA can be specified in any of the following formats:
-
a data keyword - for automatically finding physio data in a CIGAL 'pdigm' output archive file. Recognized keywords are: cardiac, respiration, gsr, eyex, eyey, pupildiam, pupilaspect
a CIGAL 'pdigm' file - use FLAG to specify which physio data to use
2 list text files - specifying amplitude and time values separately
2 'pd' records - specifying records in a CIGAL 'pdigm' file for amplitude and time values
The output of PHYSIO is one or more reference time course variables.
The FLAG argument specifies what should be done
Additional options can be specified as 2-argument pairs of the form, OPTNAME VALUE, where OPTNAME is the name of the option and VALUE is the value you want to assign for that option. The recognized option names are:
bin -
width -
spike -
smooth -
time0 - scan time 0 in secs, relative to clock time 0
tr - scan TR time (sec per volume of images)
nz - number of slices per TR
interleave - slice timing flag: 0=sequential, 1=odd then even, 2=even then odd (1st slice# = 1) (default from data hdr)
print - control output display options (default printing is to file 'physio_name.txt')
1 - print one-line summary
2 - print list of peaks found
4 - print resampled phase, rate, amplitude values
8 - print to standard output rather than default data file
16 - print RETROICOR parameters
32 - print RHVRCOR parameters
64 - omit the column header line
range - with no argument, means just report percent signal fluctuation range
range - with a number argument, minimum percent signal range needed for physio analysis (default: 2 %)
Examples:
-physio cardiac.txt 0711
Read cardiac data from 2-column text file
-physio cardiac
Automatically search for cardiac data in 'pdigm' file
-physio pd9 pd7 0712
Specify respiratory amplitude and timebase explicitly, with analysis flag
-physio respir 0 bin 0.5 print 7 name respdata
Generate resampled data every 0.5s, store in physio_respdata
See Also:
fScan Home,
fScan Manual,
CmdLineOptions,
Manual Help