The efficiency is low in part because you have only one presentation for each
event type. The efficiency will scale with number of events for a given type
and will decrease when you have more overlap in the HRFs. Whether it matters or
not depends on how you are going to analyze your data. The optseq efficiency
calculation assumes that you will use an FIR; if you are going to assume a
shape, then it does not matter so much. If you are going to combine events into
a single event type, then it does not matter so much.
On 6/3/2019 4:55 AM, Katarina Bendtz wrote:
External Email - Use Caution
Dear Douglas:
Thanks so much for your quick reply! I appreciate your help a lot! Please see
my answer below.
I have 20 trials, and two conditions, "test" and "control", with 10 trials of
each condition. In this example I only had 4 trials since I wanted to test if
the large number of events was yielding my problem. The reason why I specify
all trials as individual events is that the trials differ greatly in duration
(between 12 s and 20 s) and *all* have individual durations. I was assuming
this would be important information for the schedule optimization, but maybe
you think it is better to use the average duration of each condition (even
though that will differ from individual event durations with up to 6 s) and
then I randomimze the order of events myself?
No, you are right, it is important. I'm not sure what is going wrong here
without the full command line. optseq was not designed with this type of
application in mind, so it might not be possible.
Ok thanks, I see. Here’s a full command line (also attaching all output) where
I specified all different trials (with their specific durations but rounded to
the nearest multiple of the TR = dPSD). I do get some schedules but the
efficiency is very low. What would you recommend for me to do?
eduroam-10-200-35-57:Downloads bendtz$ ./optseq2 --ntp 1500 --tr 1.86 --psdwin
11.16 48.36 1.86 --nkeep 3 --nsearch 1000 --o test --ev control_trial_3 18.6 1
--ev control_trial_4 14.88 1 --ev control_trial_16 20.46 1 --ev
control_trial_18 13.02 1 --ev test_trial_26 18.6 1 --ev control_trial_29 16.74
1 --ev test_trial_31 18.6 1 --ev test_trial_36 20.46 1 --ev test_trial_41 16.74
1 --ev test_trial_43 18.6 1 --ev test_trial_45 16.74 1 --ev test_trial_47 18.6
1 --ev control_trial_48 16.74 1 --ev test_trial_53 13.02 1 --ev
control_trial_60 13.02 1 --ev test_trial_67 18.6 1 --ev control_trial_69 26.04
1 --ev control_trial_71 18.6 1 --ev control_trial_75 18.6 1 --ev
control_trial_79 18.6 1
INFO: Setting srand48() seed to 999910
optseq2
$Id: optseq2.c,v 2.15 2009/05/26 18:13:45 greve Exp $
NoSearch = 0
nSearch = 1000
nKeep = 3
PctUpdate = 10.000000
nCB1Opt = 0
seed = 999910
Ntp = 1500
TR = 1.86
TPreScan = 0
PSD Window = 11.16 48.36 1.86
nEvTypes = 20
EvNo Label Duration nRepsNom
1 control_trial_3 18.600 1
2 control_trial_4 14.880 1
3 control_trial_16 20.460 1
4 control_trial_18 13.020 1
5 test_trial_26 18.600 1
6 control_trial_29 16.740 1
7 test_trial_31 18.600 1
8 test_trial_36 20.460 1
9 test_trial_41 16.740 1
10 test_trial_43 18.600 1
11 test_trial_45 16.740 1
12 test_trial_47 18.600 1
13 control_trial_48 16.740 1
14 test_trial_53 13.020 1
15 control_trial_60 13.020 1
16 test_trial_67 18.600 1
17 control_trial_69 26.040 1
18 control_trial_71 18.600 1
19 control_trial_75 18.600 1
20 control_trial_79 18.600 1
PctVarEvReps = 0
VarEvRepsPerCond = 0
PolyOrder = -1
tNullMax = -1
tNullMin = 0
outstem = test
AR1 = 0
No refractory penalty
Cost = eff
OutStem = test
Summary File = test.sum
nTaskAvgs = 400
INFO: LogFile is test.log
outstem = test
5 59 0.6 8.42937e-09 8.42937e-09 1.8550 0.975 0.15632
8.42937e-08 1 1 40.9436 0
22 226 2.4 8.42937e-09 8.42937e-09 1.8550 0.975 0.15632
8.42937e-08 1 1 40.9436 0
75 756 8.4 0.0025 0.0025 1.8550 1 0 1 1 0 30.9512 0
75 1000 11.1 0.0025 0.0025 1.8550 1 0 1 1 0 30.9512 0
INFO: searched 1000 iterations for 0.185833 hours
INFO: 1.49477 iterations per second
INFO: 997/1000 schedules were ill-conditioned
outstem = test
>
>
> I get:
>
>
> NFO: searched 1000 iterations for 0.010556 hours
> INFO: 26.3158 iterations per second
> INFO: 1000/1000 schedules were ill-conditioned
> ERROR: all schedules found were ill-conditioned. This
> probably means that you need more scan time (ie, a
> greater number of time points) or fewer repetitions.
>
> (I'm running on a macOS Mojave version 10.14.3. )
>
> But it's obviously not the ntp that is the problem since I put an
> extra long time there that cover the event durations by far.
>
> Is there any way I can troubleshoot more efficiently myself? The log
> file doesn't tell me anything.
>
> Very happy for any advice,
>
> All the best,
>
> Katarina
>
>
>
>
> Katarina Bendtz, Ph.D. (particle physics)
> Postdoctoral researcher in cognitive neuroscience
> Department of Psychology, Stockholm University
>
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