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').

pynifti_pst 0.20100412.1                           April 2010                                     PYNIFTI_PST(1)