Re: [Freesurfer] Event-Related design and jitter in stimulus onset

By default, optseq uses an internal clock synchronize to the TR (so events can only start on the TR). This can be changed by setting dPSD (eg, to 1). This would allow the NULL events to be multiples of 1 instead of 2. The PSD is specified in seconds. doug

SHAHIN NASR wrote:

optseq2 --ntp 132 --tr 2 --tsearch 0.5 --ev C1 6 4 --ev C2 6 4 --ev C3 6 4 --ev C4 6 4 --ev C5 6 4 --ev C6 6 4 --ev C7 6 4 --ev C8 6 4 --ev C9 6 4 --ev C10 6 4 --nkeep 10 --psdwin 10 16 --o Opt_Par_2nd

On Fri, Dec 9, 2011 at 2:03 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

What is your command line?


SHAHIN NASR wrote:

          Thanks Doug.
       In my experiment, each trial (event) consists of 1 sec
    stimulus presentation and 5 sec blank interval (TR=2). I have
    also added a condition with just blank presentation which will
    be repeated as much as other events.

       I have used optseq2 commands to generate the trial
    sequence. But I faced two problem/questions:

       1) Using this command, I expected to see a Null event
    (other than my blank condition) with variable length
    (irrespective of TR) between other trials. But to my surprise,
    length of the Null event was always a multiplication of TR. Is
    that correct?


       2) Also, for "psdmin psdmax" I wasn't sure if they are
    number of TRs or number of seconds and what is a safe window
    length when my stimuli are very simple visual objects (and no
    cognitive task).

    Once again, thanks for your help.



    On Fri, Dec 9, 2011 at 1:10 PM, Douglas N Greve
    <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>> wrote:

       Hi Shahin, there are several ways to answer this question.
    If you
       are going to analyze assuming a shape to the HRF, then the
    actual
       delay between stimuli is technically not important (though
    4s will
       be good to avoid attenuation in the following stimulus). If
    you're
       using an FIR model of the HRF (no assumed  shape), then I
    usually
       advise that you have, in total, as much time spent on
    fixation (or
       whatever your null stimulus is) as you have for any other
       stimulus. You can use optseq to compute the actual schedule.
       doug


       SHAHIN NASR wrote:

           Hi Surfers,

             It is my first experience with Event-related
    paradigms. In
           my experiment, trials take minimum 6s (TR=2s). I wonder
    what
           is the optimum variable delay between trials to be able to
           analyze data without any confound.

           Regards

           --         Shahin Nasr

           PhD in Cognitive Neuroscience
           Martinos Imaging Center, MGH
           Harvard Medical School


       --     Douglas N. Greve, Ph.D.
       MGH-NMR Center
       greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
       Phone Number: 617-724-2358 <tel:617-724-2358>
    <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422
    <tel:617-726-7422>
       <tel:617-726-7422 <tel:617-726-7422>>

       Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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    -- 
    Shahin Nasr

    PhD in Cognitive Neuroscience
    Martinos Imaging Center, MGH
    Harvard Medical School


-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422
<tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

-- Shahin Nasr

PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School