Re: [HCP-Users] How to deal with the slight delay in 7 HCP Eprime tasks

[Burgess, Gregory]

On Feb 26, 2018, at 8:32 PM, HMZ > wrote:

Hi Greg,
Thanks a lot for your reply. To express my question clearly, I compared the 
time points when cues appear in WM task. In the following table, the actual 
time points extracted from the EVs of sub 100307 are shown in the first column, 
and the corresponding time points in the second column are calculated by task 
design (based on the block duration and fixation duration decribed in paper). 
There are slight delay in every block, and the delay will accumulate to several 
seconds at the end of task, which is the same in my experiment with HCP tfMRI 
Eprime program.

E-Prime experiences small delays in timing, because some Windows OS processes 
take precedence over all other applications running. The consequence is that 
E-Prime must wait for Windows to finish, introducing occasional delays on the 
order of milliseconds. Those millisecond delays add up over time, so that the 
onset of the final events may differ from the design by a few seconds.

That is why we release the EV files, and the corresponding TAB.txt files, which 
output the actual timing for each scan run after these variable delays occur.


I guess the time error comes from tiny delay in each trial because the time 
mode of some stim slides are "event" mode, which will not compensate the 
“SyncSlide.OnsetDelay”.
I'm wondering whether it is matter if the task programs are used in different 
labs and the "OnsetDelay" in different labs are a little different. For 
example, there is around 5 sec difference in total time of WM.
I want to seek your advice on this matter. Any relevant information would be 
very helpful. Thanks a lot!


I apologize that I don’t understand your statements above. But, you should use 
the timing information that we provide (EV files and TAB.txt files) to avoid 
any discrepancies in your models.


--Greg


Greg Burgess, Ph.D.
Staff Scientist, Human Connectome Project
Washington University School of Medicine
Department of Psychiatry
Phone: 314-362-7864
Email: gburg...@wustl.edu




[X]

--
Meizhen Han
PhD Candidate
Center for MRI Research
Peking University
Beijing, China

At 2018-02-24 01:57:49, "Burgess, Gregory" 
> wrote:
There is no difference between the duration of the E-Prime tasks and the 
duration of the BOLD time series from the scan. There is likely a 
misunderstanding of what the duration should be, but I can’t help without 
knowing specifically what doesn’t line up in your opinion.

There have been two things that have confused other users:
1) The “Run Duration” reported in HCP publications is the total duration 
reported by the scanner. But, that includes ~9.36s for scanner preparation and 
collection of the SBRef volume. That time period occurs before the BOLD time 
series and before the fMRI task begins, and should not be factored into task 
timing.
2) At the beginning of most tasks (all but LANGUAGE), there is an 8s 
“countdown” period before the first event in the task. Those 8s are included at 
the beginning of the BOLD time series image, and are included in the timing 
information in the EV files. So, if you haven’t included them in your 
estimation of the task timing, you might think that the task was too short or 
the scan too long.

Please review Barch et al. (2013) which includes more detailed description of 
the tasks, and that should help you understand the timing information that 
we’ve released in the EV directories in the packages.

--Greg


Greg Burgess, Ph.D.
Staff Scientist, Human Connectome Project
Washington University School of Medicine
Department of Psychiatry
Phone: 314-362-7864
Email: gburg...@wustl.edu

On Feb 23, 2018, at 4:56 AM, HMZ > wrote:

Dear HCP experts,

This is Meizhen Han from Peking University.

Thanks for releasing the 7 fMRI tasks written in Eprime software used in Main 
HCP. I downloaded and run them on the Sinorad fMRI Stimili System in our lab. I 
find there is a slight difference between the actual time duration and the 
theoretical time duration calculated by task design. In addition, according to 
the related articles published by HCP groups, the scanning time for each task 
is a little longer (several seconds) than the theoretical time.

I’m wondering whether did you encounter this slight delay in your experiment 
and data analysis, and how did you deal with it.

Any relevant information would be very helpful. Thanks in advance!

Meizhen Han
PhD student
Center for MRI Research
Peking University

Re: [HCP-Users] 7T resting state data

[Elam, Jennifer]

Hi Janine,

There was a bug in the processing of the 7T functional data we originally 
released, so we have reprocessed the data from all 184 subjects and are 
preparing the data for release, likely by the end of this month.


Best,

Jenn

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org



From: hcp-users-boun...@humanconnectome.org 
 on behalf of Janine Bijsterbosch 

Sent: Thursday, March 8, 2018 7:14:53 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] 7T resting state data

Hi,

When I try to download the 7T data from connectome DB all the relevant packages 
are greyed out and no links are available for these downloads. Could you let me 
know when the fix-cleaned 7T resting state data will be available for download 
please?

Thanks!

Best wishes,

Janine


-
Dr Janine Bijsterbosch
Postdoctoral Researcher
FMRIB Centre, University of Oxford
John Radcliffe Hospital
Oxford, United Kingdom
janine.bijsterbo...@ndcn.ox.ac.uk


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[HCP-Users] 7T resting state data

[Janine Bijsterbosch]

Hi,

When I try to download the 7T data from connectome DB all the relevant packages 
are greyed out and no links are available for these downloads. Could you let me 
know when the fix-cleaned 7T resting state data will be available for download 
please?

Thanks!

Best wishes,

Janine


-
Dr Janine Bijsterbosch
Postdoctoral Researcher
FMRIB Centre, University of Oxford
John Radcliffe Hospital
Oxford, United Kingdom
janine.bijsterbo...@ndcn.ox.ac.uk


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