The PSD Window is the time over which you expect the hemodynamic response to last. If your event lasts 3 sec, I would put 21, so "--psdwin 0 21 3". If you want to constraint the ISI to be between 5.5 and 8.5 sec, then use "--tnullmin 5.5 --tnullmax 8.5"
Also, you need at least 3*20*(3+7) = 600sec = 200 time points of scanning time
doug
On 06/10/2013 01:47 PM, A a wrote:
Correction
This is the lats code :
optseq2 --ntp 140 --tr 3 --psdwin 6 15 3 --ev ev20 3 20 --ev ev40 3 20 --ev ev60 3 20 --nkeep 3 --o OptSeq_TRIALS/trial_squ --nsearch 10000
So The duration is 3 seconds for each and each repeat it 20 times. What I need is to change/add the ISI to be 7 + or - 1.5 seconds.
Any help please ?
Another point is about the psdwin, I am not sure what exactly it represents. I saw your slides but I thought this should also change the ISI,. Can you comment on it please ?
Thanks
AS
On Mon, Jun 10, 2013 at 5:49 PM, fMRI <fmri2013@gmail.com mailto:fmri2013@gmail.com> wrote:
Dear Prof Douglas, Thanks for your response. I managed to do the following: optseq2 --ntp 140 --tr 3 --padwin 0 12 3 --ev ev15 --ev ev30 --ev ev45 --nkeep 3 --o trial --nsearch 10000 Now what I really want to do is to make the ISI 7 seconds + or - 1.5 seconds. I am not sure how I should use the percentage option if this is what I should change plus the ISI time? I hope this clarifies it more Regards, AS On 10 Jun 2013, at 16:21, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > Hi, can you at least come up with an optseq2 command line that I could > then help you with? There are lots of examples on the web page. You > should be able to get to a point where you have an error. > thanks > doug > > > On 06/10/2013 05:14 AM, fMRI wrote: >> Hello all, >> >> This is my first question in this list and it is about OptSeq2. >> >> I am nee to this command. >> >> In brief, I wish to insert the following but Some of them I could not handle it: >> >> My experiment has three conditions although I will later specify them as one condition: >> >> Moving hand at three different target level ( say 10 20 30). Then I will model them as a one condition and enter the parametric response as a first order polynomial effects. >> >> My design will have two columns : main effect of moving hand and the 1 order. >> >> My contrast will be like this [1 0; 0 1] >> >> This is what I would like to optimize using OptSeq2: >> >> Event design >> 1) ISI 6 seconds + or - 1.5 seconds ( I could not do this >> 2) TR 3 >> 3) volumes 150 >> 4) 45 hand movement; 15 at each target level ( I could not do this ) >> 5) each movement lasts for 3 seconds >> >> I am not sure whether I should use null events or the Period between movement is enough. >> >> Also my main aim is to optimize the best design in terms of detection. >> >> Please any guide or help >> >> Thanks >> >> >> AS >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. >