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normerp - normalize ERP data using calibration pulses
normerp
input_data output_data [options]opt
normerp is used to equalize
the difference in gain between channels of ERP data and set the absolute
voltage per point value. These inter-channel gain inequalities can arise
at the polygraph, tape recorder, A/D converter, etc. Standard procedure
is to record calibration pulses (condition code 0, bin 0) of known amplitude
and polarity on all channels, and then scale the data after they are averaged
so that the calibration pulses in all channels are of the same size. The
absolute polarity and resolution of the data are fixed at this point. normerp
performs this function by displaying the calibration pulses (bin 0 by default
in the continuous data system) on the display_device, taking the input
data the from input_data file and placing the normalized data in the output_data
file. The user specifies the points on the calibration pulses which should
be used to compute the size of the calibration pulses. Two cursors are used
for this purpose; the voltages at the cursors determine the size of the
calibration pulses. Optionally one can request that a certain number of
points around each cursor be averaged together to improve resolution and
accuracy. This is especially useful for noisy calibration data. The program
is (purportedly) self-explanatory in interactive usage, although problems
in determining the polarity of the cal. pulses can arise.
On invocation,
normerp checks that the input data file can be opened, an X window display
device is available, and that the output data file does not already exist.
Then it displays the calibration bin on the display. Next, the user is
prompted to enter various parameters regarding the calibration pulses and
desired resolution of the output data. These include the cursor locations,
size of the calibration pulses (in microvolts), the polarity of the data,
and the eventual absolute resolution of the data in points per 10 microvolts.
At this point normerp enters an interactive mode in which a menu of possible
options is displayed which allows the user to specify how many points to
average around the cursors, change the display gain, change the cursor
locations, etc. In the interactive mode, no returns from the keyboard are
required. When finally satisfied that the data are properly parameterized,
selecting the menu option (o)
k to normalize data will cause normerp to
exit the interactive mode and prompt: Are you sure? Any response other
than yes (or something beginning with a "Y") will cause reversion to interactive
mode.
Some explication of the issues involved in supplying parameters to
normerp is in order. Positive "up" on the screen implies that positive point
values are active electrode positive voltages. Thus, if one connects the
positive lead of the calibration box to the same input as the active scalp
site(s) and the display on the screen during normalization shows these
pulses to be "down", then the polarity of the data is positive down, and
a -1 should be specified to normerp.
The desired resolution of the data is
also fixed by the user using a parameter specifying the number of points
per 10 microvolts. If the un-normalized data have more resolution than results
after normalization using the specified number of points per 10 uVolts,
it is lost; and while specifying a large number of points per 10 uVolts
will magnify the data, the underlying accuracy/resolution can be no greater
than was present in the un-normalized data.
To enhance the generality of
the program and allow recovery from abnormal situations, a number of options
are available on invocation. These include:
- -a N
- Average N points on either
side of the cursors (including the point at the cursor) for a total of
(2N+1) points.
- -s display_scaling_factor
- The display_scaling_factor is an
arbitrary number whose default value is 5. Hence, to double the size of
the display, enter 10, etc.
- -f cal_file
- Use cal_file for the calibration
pulses used to calculate the normalization coefficients. The data to be
normalized are still drawn from the input_data file and the normalized
data placed in output_data. This option is included to allow one to recover
from situations in which the calibartion pulses somehow didn’t make it into
the input_data file. This is a dangerous option - one must be sure nothing
changed between the time the subject’s data were recorded and the calibration
pulses were recorded. Also, not that the cal_file CANNOT HAVE BEEN NORMALIZED
before being used in this manner; if it has been the between channel gain
differences will already have been eliminated!
- -c cal_bin
- Employ cal_bin
as the bin in the input_data file containing the cal pulses. This is normally
uses for test and diagnostic purposes only.
- -n low_cursor hi_cursor cal_size
polarity resolution
- This option causes normerp to operate silently; no
prompting is perform and no display is employed. It is used when one is
sure everything is O.K. and the normalization parameters listed are known
in advance. It is most useful in an automated shell script.
- /usr/local/erp/lib/graphicdevs
- plotting device data base and filter information
specific plot device "normerpxwin" defined in here
erp_overview(7)
As usual, meant to be self-explanatory and occurring because
of so many sources they can’t all be listed. The most cryptic is:
Cal on channel xx is mighty weenie
meaning the difference in the pulses at the two cursors was less than 100
points. Hence, the data cannot be more accurately normalized than +_ 1
%.
Overflow can occur and causes normerp to print:
normerp - overflow on bin XX.
It may be possible to avoid this by specifying a smaller value for points
per 10 uVolts. This sometimes occurs when a bin has very few sums. If overflow
does occur and the data are not repaired, do not attempt to plot that bin.
Jonathan C. Hansen UCSD ERPL
It is not possible to set cursors
separately for each channel of data.
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