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’).