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 numbers 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  single  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 stimulations ('mean'). Other possibilities
              are the standard deviation ('std') and standard error ('sde').