On 5/31/2019 2:18 AM, Katarina Bendtz wrote:
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Dear Douglas:
Thank you so much for your reply. It is however still not clear to me how this works. Pls see my replies below.
All the best and many thanks for your time,
Katarina
PS. I'm registered to the list so I don't know why my mail is listed as external, sorry.
On 5/29/19 1:05 PM, Katarina Bendtz wrote:
External Email - Use CautionDear experts:
I'm using the optseq2 version 2.15 2009/05/26. I have three questions:
- How does the [PSDmin, PSDmax] relate to the jittered intertrial intervals?
The PSDmax sets the maximum window overwhich jitter needs to be considered. It is assumed that the hemodyn response will be 0 after PSDmax and so that jitter will not matter beyond this time.
Why then do I get schedules with intertrial breaks (NULLs) with durations longer than PSDmax? Isn't that just a waste of time then? Yes, it depends on how long the scan is (TR*NumberOfTRs) and how many trials you have. If you have too few trials, then you will get "empty" space.
- I have stimuli of between 12 and 20 seconds, where the part of my stimulus that I want to measure is in the last 5 seconds or so. What should I put my dPSD window to? It's both a matter of that the signal starts later than the stimulus presentation, so I guess I would have a PSDmin of a couple of seconds, but how do I handle the variation in stimuli lengths?
You need to have the PSD window completely cover the hemodyn response regardless of what you are interested in.
This is counting from the onset time of the stimuli right? In that case I will have to put the PSDmin to the time when my target starts?(My stimuli are dialogues: Context (appr. 12 s) + Q (appr. 3 s) + A (appr. 3 s), and I only want to measure the answer, so I should then put PSDmin to 12 s + 3 s = 15 s? And then PSDmax to PSDmin + (HRF response time)? No, you have to put PSDMin=0. All those other events will produce a hemodyn response regardless of whether you want to measure it or not.
- As mentioned above I have quite a large variation between my stimuli. When I try to specify them individually (about 25) I always get that all schedules are ill-conditioned. Is this because such schedules are generally hard to optimize?
Schedules with lots of different conditions are hard to optimize.
- I quite often get that all schedules are ill-conditioned, but there is no information in the log file that tells me what is wrong. Example:
./optseq2 --ntp 1500 --tr 1.86 --psdwin 0 22.32 0.93 --nkeep 3 --nsearch 1000 --o test --ev control_trial_1 16.74 1 --ev control_trial_3 18.6 1 --ev control_trial_7 18.6 1 --ev test_trial_11 16.74 1
You only have 1 event for each condition. Surely you must have more?
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.
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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