Issue 65 in neurorighter: SALPA not properly blanking stim artifacts when using 15 kHz sampling rate

[neuror...@googlecode.com]

Status: New
Owner: ----
Labels: Type-Defect Priority-Medium

New issue 65 by jonathan...@gmail.com: SALPA not properly blanking stim
artifacts when using 15 kHz sampling rate
http://code.google.com/p/neurorighter/issues/detail?id=65

What steps will reproduce the problem?
1. Do an open-loop stim protocol, using SALPA and a 15 kHz sampling rate
(or at least some value not equal to 25 kHz)

What is the expected output? What do you see instead?
Expect to see stim artifacts blanked. Blanking does not occur properly.
Please see attached figure.


What version of the product are you using? On what operating system?
v 1.0.2.521 , winXP SP3, 32-bit

Please provide any additional information below.
Attached a figure to help illustrate what I am seeing for raw traces and
the (improperly) blanked SALPA traces immediately after a stimulus. Figure
shows raw data and same data segment from .salpa file.


Attachments:
stimArtifact_salpa.tif 82.9 KB

[neuror...@googlecode.com]

Comment #1 on issue 65 by jonathan...@gmail.com: SALPA not properly

blanking stim artifacts when using 15 kHz sampling rate
http://code.google.com/p/neurorighter/issues/detail?id=65

I note that in the original SALPA paper, all data was presented for fs = 25
kHz and we just copied the parameters from that paper. Doug Bakkum noted to
me, anecdotally, that it was easy to break SALPA with different sampling
rates.

Riley, you have the most insight here. What do you think the issue is? It
seems like SALPA thinks it has a decent fit very prematurely.

[neuror...@googlecode.com]

Comment #2 on issue 65 by RZellerT...@gmail.com: SALPA not properly

blanking stim artifacts when using 15 kHz sampling rate
http://code.google.com/p/neurorighter/issues/detail?id=65

Righto- I'll take a look at this Thursday.

[neuror...@googlecode.com]

Comment #3 on issue 65 by jonathan...@gmail.com: SALPA not properly

blanking stim artifacts when using 15 kHz sampling rate
http://code.google.com/p/neurorighter/issues/detail?id=65

Riley, what is the status here?

[neuror...@googlecode.com]

Comment #4 on issue 65 by RZellerT...@gmail.com: SALPA not properly

blanking stim artifacts when using 15 kHz sampling rate
http://code.google.com/p/neurorighter/issues/detail?id=65

still need to look into this on the rig, however:
biggest issue is that the artifact isn't being detected, either through
thresholding or through the 'stim' stream. Whether or not SALPA is fitting
prematurely will be seen after we get blanking working again.

Were their areas of the SALPA trace that were blanked, just not where the
stimuli occurred?

Were stimuli recorded at all during this experiment?

Note that several of the SALPA parameters are based on samples, so changing
sampling rate would very quickly alter their meaning. It would probably be
a good idea to switch to 'ms' as a measure for the curve length, blanking
period, etc.

[neuror...@googlecode.com]

Comment #5 on issue 65 by jonathan...@gmail.com: SALPA not properly

blanking stim artifacts when using 15 kHz sampling rate
http://code.google.com/p/neurorighter/issues/detail?id=65

No. (I've previously verified that the stimulation times stay synced to the
expected delivery times to within about 20 us over an hour, so I've stopped
worrying about them).



Yes- agree. I typically use a 15 kHz sampling rate, instead of 25 kHz, and
have always adjusted the default parameters appropriately.

[neuror...@googlecode.com]

Comment #6 on issue 65 by RZellerT...@gmail.com: SALPA not properly

blanking stim artifacts when using 15 kHz sampling rate
http://code.google.com/p/neurorighter/issues/detail?id=65

Using the SALPA parameters you describe (45 sample half width, 0 post-peg,
6 minimum peg, 3 pre peg, 6 min symmetric, right?), SALPA was able to run
correctly on one of our rigs (AD rig).
However, SALPA behaved as you described in your figure if electrical
stimulation input was turned off. Note that this only occurred if I
disabled the 'Stimulation Timing' input in the 'Aux. Input' page of the
Hardware Settings. The Electrical Stim 'real time data stream' does not
need to be activated (on the 'real time' page of Hardware Settings), and
the Electrical Stim data data stream does not need to be recorded (in the
Recording Stream Setup dialog).
SALPA gets a signal from the electrical stim recording set up, which it
uses as way to determine when to blank the signal, IE when the signal is
too distorted by stimulation artifact to recover. When the electrical stim
input is not turned on, SALPA doesn't get that signal and just performs
it's usual curve fitting.
Given that you aren't recording electrical stimulation, that seems like a
probably culprit.
Thanks a bunch and I'm sorry about the extreme delay on this.