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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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 > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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> > <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> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > The information in this e-mail is intended only for the > person to > whom it is > addressed. If you believe this e-mail was sent to you in > error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was > sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
