pynifti_pst(1) [debian man page]

PYNIFTI_PST(1)							   User Commands						    PYNIFTI_PST(1)

NAME

       pynifti_pst - compute peristimulus timeseries of fMRI data

SYNOPSIS

       pynifti_pst [options] <4dimage> <outfile> <vol_id | filename> [...]

DESCRIPTION

       pynifti_pst computes the peristimulus signal timecourse for all voxels in a volume at once. Stimulus onsets can be specified as volume num-
       bers or times (will be converted into volume numbers using a supplied repetition time).	Onsets can be specified directly  on  the  command
       line,  but  can	also be read from (multiple) files. Such file are assumed to list one onset per line (as the first value). Empty lines are
       ignored. This enables pynifti_pst to use e.g. FSL's custom EV files. If several files are specified, the read onsets are combined to a sin-
       gle  onset  vector.  pynifti_pst  writes a 4d timeseries image as output. This image can e.g. be loaded into FSLView to look at each voxels
       signal timecourse in a certain condition by simply clicking on it.

OPTIONS

       --version
	      show program's version number and exit

       -h, --help
	      show this help message and exit

       --verbose
	      print status messages

       -n NVOLS, --nvols=NVOLS
	      Set the length of the computed peristimulus signal timecourse (in volumes). Default: 10

       -t, --times
	      If supplied, the read values are treated as onset times and will be converted to volume numbers. For each onset the volume  that	is
	      closest in time will be selected. Volumes are assumed to be recorded exactly (and completely) after tr/2, e.g. if 'tr' is 2 secs the
	      first volume is recorded at exactly one second.  Please see the --tr and --offset options to learn how to adjust the conversion.

       --tr=TR
	      Repetition time of the 4d image (temporal difference of two successive volumes). This can be used to override the setting in the	4d
	      image.  The  repetition  time is necessary to convert onset times into volume numbers. If the '--times' option is not set this value
	      has no effect. Please note that repetitions time and the supplied onsets have to be in the same unit.  Please note, that if  --times
	      is given the tr has to be specified in the same unit as the read onset times.

       --offset=OFFSET
	      Constant	offset	applied  to the onsets times when converting them to volume numbers. Without setting '-- times' this option has no
	      effect'.

       -p, --percsigchg
	      Convert the computed timecourse to percent signal change relative to the first (onset) volume. This might  not  be  meaningful  when
	      --operation is set to something different than 'mean'. Please note, that the shape of the computes timeseries heavily depends on the
	      first average volume. It might be more meaningful to use a real baseline condition as origin. However, this is  not  supported  yet.
	      Default: False

       --printvoxel=PRINTVOXEL
	      Print  the  peristimulus timeseries of a single voxel for all onsets separately. This will print a matrix (onsets x time), where the
	      number of columns is identical to the value of --nvols and the number of rows corresponds to the number of specified onsets.   (e.g.
	      'z,y,x')

       --operation=OPERATION
	      Choose  the math operation that is performed to compute the peristimulus timeseries. By default this is the mean across all stimula-
	      tions ('mean'). Other possibilities are the standard deviation ('std') and standard error ('sde').

pynifti_pst 0.20100412.1					    April 2010							    PYNIFTI_PST(1)

Check Out this Related Man Page

AUBIOONSET(1)						      General Commands Manual						     AUBIOONSET(1)

NAME

       aubioonset -- a command line tool for real time onset extraction

SYNOPSIS

       aubioonset [options] [-i soundfile]

DESCRIPTION

       aubioonset attempts to detect onset times, the beginning of discreted sound events, in audio signals.

       When  started  without  an  input file argument (--input), aubioonset creates jack input and output ports. When an input file is given, the
       results are given on the console.

OPTIONS

       This program follows the usual GNU command line syntax, with long options starting with two dashes (`-').  A summary of options is included
       below.

       -i   --input filein
		 Run analysis on this audio file. Most common uncompressed formats are supported.

       -o   --output fileout
		 Save results in this file. The file will be created on the model of the input file. Results are marked by a short wood-block sam-
		 ple.

       -O   --onset mode
		 The onset detection function to run. Available functions are complexdomain, hfc, phase, specdiff, energy, kl and mkl. By default,
		 both Kullback Liebler (kl) and complex domain are used in parallel.

       -t   --threshold value
		 Set  the  threshold  value for the onset peak picking. Typical values are within 0.001 and 0.900. Default is 0.1. Lower threshold
		 values imply more onsets detected. Try 0.3 in case of over-detections.

       -j   --jack
		 Run in jack mode (default when started without input file) and creates a midi output.

       -v   --verbose
		 Show results on the console (default).

       -h   --help
		 Show summary of options.

BUGS

       For now the program has only been tested on audio signals sampled at 44.1 kHz.

SEE ALSO

       aubiotrack(1) aubionotes(1) aubiocut(1) aubiopitch(1)

AUTHOR

       This manual page was written by Paul Brossier (piem@altern.org). Permission is granted to copy,	distribute  and/or  modify  this  document
       under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation.

       On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

																     AUBIOONSET(1)

Linux and UNIX Man Pages

pynifti_pst(1) [debian man page]

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