pta

Compute the mean response associated with a particular stimulus pattern.

Options:

• simple - write PTA PSTH, can do peak stats.
• multi - advanced analysis for multi-dim stim (like ran_sin). (Simple patterns require only 'multiflag' below)
• stimulus - write PTA average of STIMULUS - to check for stimulus correlation to itself (e.g., trigger on m-seq pattern 00011 to see what comes after it). Probably only works for single pattern (e.g. "pattern xxxxx").
• raster - write raster plots and PSTH. The PSTH is simply the count of the number of spikes at each millisecond bin.
• write_stim - plot the stimulus sequence for all trials in the first group, then exit. A HACK.
• peak_stat - compute statistics of PTA peak, and var/mean for count. The PTA is smoothed with a Gaussian of SD 'sigma' if 'sigma' is > 0.0 before statistics are extracted. The window for the statistics is defined by 'peak0' and 'peakn'. If these are not set, the default stat window is 2*width, starting at tpeak - width.

    cell cond peak tpeak left right width t_mean t_SD prob n mean var var/mean
  

  • cell - input filename w/o path?
  • cond - description of the group of trials
  • peak - maximum spike probability (within 1 ms bin), peak is found w/i "pta_start", "pta_period" window.
  • tpeak - time of peak (ms)
  • left - time of left half-rise (ms)
  • right - time of right half-rise (ms)
  • width - 'right' - 'left' (ms)
  • t_mean - mean of first spike times
  • t_SD - SD of first spike times
  • prob - probability of at least one spike in window
  • n - number of times the pattern was found
  • mean - spike count mean
  • var - variance of spike count
  • var/mean - ratio of spike count var/mean (or \N if mean=0)

• precision - compute SD to first spike and probability of response within the time window. PTA window is analysis window. The resulting output file has the following line format:

    cellname  mean  SD  reliability  n  condition
  

  • cellname - input filename w/o path?
  • mean - mean of first spike times
  • SD - SD of first spike times
  • reliability - probability of at least one spike in window
  • n - number of times the pattern was found
  • condition - description of the group of trials

• pndiff - compare null -> pref and pref -> null transitions.
• terndiff - plot differences of PTA for a list of ternary patterns.
• plotnbit - plot PTA for all patterns with n bits.
  • trialnum [k] - process only trial k in group. k = -2 indicates to use last trial in group. k= -1 is default, i.e., process entire group.

Parameter definitions:

• pta_start - Start time for averaging window.
• pta_period - Duration of averaging window.
• sem_flag - (0) 1-SEM instead of SD for *float* PTAs.
• toffset - Offset time added to stimulus onset time for PTA.
• pta_scale_samp - 0-no scaling (prob), 1-scale by sampling (spk/s)
• stim_chan [chan_name] - get stimulus from named channel.
• pattern - Pattern to search for. If using 0,1,2,3... set ternary to 4. Use with outtype simple.
• pat_invert - exchange `1' and `0', or `p' and `n'.
• pattern_range -
• nbit -
• deriv -
• ternary
  • 0 - interpret stim as 0,1 (-1 gets set to 0)
  • 1 - interpret stim as -1,0,1
  • 4 - interpret stim as single digits: 0,1,2,3,...
• gaussian -
• multiflag - (0) 1-multi-dimensional stimuli, e.g. 'ran_sin'

  When this flag is set to 1, the pattern parameter should be given as a string of the following form:

      pattern o1p1-o2p2-b
  

  which is a list of stimulus identifiers separated by dashes. Each identifier is either 'b', standing for a blank (or control) stimulus, or it specifies several numbers, which are indices into the multi-dimensional stimulus (indices start at 1). The letters 'o' and 'p' can be any letters, and should be chosen as a useful memory aid.

  Also, the parameter stim_type should be specified and stim_dt (see documentation for the sta_multi analysis type).

• seedname - Specify name of randomization seed parameter [seed is default]
• stim_dual_to_4state - If there are two random sequences that are the same except for the seed, then this can specify the second seed name, and the stimulus will be turned into a 4-value stimulus (0,1,2,3).
• jmin -
• jmax -
• discflag -
• sampling -
• sigma -
• start_chan -
• start_value -
• peak0 - (default 0) behavior is analysis dependent.
• peakn - (default 0) behavior is analysis dependent. If this value is non-zero, peak statistics will be computed.
• peak_frac1 - (default 0.05) to find 5%, or other, rise to peak.
• peak_frac2 - (default 0.5) to find 50%, or other, rise to peak.
• peak_mark - (def 0) 1-plot three markers to indicate peak stats.
• plot_diff - followed by a list of (paired) plot index values, or '0' to print a list of plot indices and pattern values. CURRENTLY WORKING FOR 'SURR4ST' ONLY, NOT FOR 'PTA'.
• The .stat file will contain for each plot:
  • stat filename
  • input filename without path
  • pattern difference string, e.g., 02-00
  • number of times the first pattern was found.
  • time of rise to 'peak_frac1' (float)
  • time of rise to 'peak_frac2' (float)
  • time of peak (int)

Example:

#
#  PTA analysis for all conditions in a matrix file.
#  Time zero is second sync.
#
pta
group 2 min_wvln max_jump
peak_stat

start_chan sync0
start_value 2
pta_start 0
pta_period 100
pattern 0000110