User Tools

Site Tools


jvs:fscan:manual:chapter2:physio

fScan Reference Manual, Chapter 2 (CmdLineOptions): pysio

Physio -- Analyze physiological waveforms

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 2-column text file - time/amplitude order is default (see Text file 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

  • FLAG - (values above 7 can be combined by addition)
    • 1 - cardiac
    • 2 - respiration
    • 3 - gsr
    • 4 - eyex
    • 5 - eyey
    • 6 - pupildiam
    • 7 - pupilaspect
    • 010 - identify peak values
    • 020 - identify trough values
    • 040 - identify zero crossings (050-rising, 060-falling)
    • 0100 - generate resampled phase values
    • 0200 - generate resampled rate values
    • 0400 - generate resampled amplitude values
    • 01000 - calculate the amplitude range
    • 010000 - flip X/Y axes

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

jvs/fscan/manual/chapter2/physio.txt · Last modified: 2014/08/04 16:03 (external edit)