compute peristimulus timeseries of fMRI data
[options] <4dimage> <outfile> <vol_id | filename> [...]
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.
show program's version number and exit
- -h, --help
show this help message and exit
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.
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.
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
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.
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').