Dear Doug, Thanks you for your e-mail and sorry for the inconvenience. Here is the code again.
In this line of code we included the fixed duartion of the fix (1.0) in the event duration specification (summing to 5.0) and asked Optseq to insert null events of a minimum duration of 0.0 in 25% of the total scanning time: --ntp 255 --tr 2.0 --tprescan 4.0 --psdwin 0.0 16.0 1.0 --ev Gain2 5.0 8.0 --ev Gain4 5.0 8.0 --ev Gain6 5.0 8.0 --ev Gain8 5.0 8.0 --ev Loss2 5.0 8.0 --ev Loss4 5.0 8.0 --ev Loss6 5.0 8.0 --ev Loss8 5.0 8.0 --ev Catch 5.0 8.0 --tnullmin 0.0 --tnullmax 6.0 --tsearch .25 -–focb 10 –-ar1 .37 --evc 1 1 1 1 -1 -1 -1 -1 0 --evc -1.5 -.5 .5 1.5 -1.5 -.5 .5 1.5 0 --evc -1.5 -.5 .5 1.5 1.5 .5 -.5 -1.5 0 --cost eff --nkeep 3 --o output_test2 In this line of code we did not include the fixed duration of the fix (1.0) in the event duration specification, but instead asked Opseq to insert null events of at minimum 1.0 sec: --ntp 255 --tr 2.0 --tprescan 4.0 --psdwin 0.0 16.0 1.0 --ev Gain2 4.0 8.0 --ev Gain4 4.0 8.0 --ev Gain6 4.0 8.0 --ev Gain8 4.0 8.0 --ev Loss2 4.0 8.0 --ev Loss4 4.0 8.0 --ev Loss6 4.0 8.0 --ev Loss8 4.0 8.0 --ev Catch 4.0 8.0 --tnullmin 1.0 --tnullmax 6.0 --tsearch .25 -–focb 10 –-ar1 .37 --evc 1 1 1 1 -1 -1 -1 -1 0 --evc -1.5 -.5 .5 1.5 -1.5 -.5 .5 1.5 0 --evc -1.5 -.5 .5 1.5 1.5 .5 -.5 -1.5 0 --cost eff --nkeep 3 --o output_test3 Since the former code yielded an error, we cut down the number of time points, in the following code. This worked, but no longer yielded extra null events in 25% of the scan time, because scan down was less now. --ntp 180 --tr 2.0 --tprescan 4.0 --psdwin 0.0 16.0 1.0 --ev Gain2 4.0 8.0 --ev Gain4 4.0 8.0 --ev Gain6 4.0 8.0 --ev Gain8 4.0 8.0 --ev Loss2 4.0 8.0 --ev Loss4 4.0 8.0 --ev Loss6 4.0 8.0 --ev Loss8 4.0 8.0 --ev Catch 4.0 8.0 --tnullmin 1.0 --tnullmax 6.0 --tsearch .25 -–focb 10 –-ar1 .37 --evc 1 1 1 1 -1 -1 -1 -1 0 --evc -1.5 -.5 .5 1.5 -1.5 -.5 .5 1.5 0 --evc -1.5 -.5 .5 1.5 1.5 .5 -.5 -1.5 0 --cost eff --nkeep 3 --o output_test4 I hope this is helpful in understanding our problem and helping us out. Thank you for your time! Best, Laura 2013/6/7 Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Hi Laura, can you just cut and paste the command line into the email? > There are some funny characters in that file you sent > doug > > On 06/07/2013 12:09 PM, Laura Dekkers wrote: > >> Dear Doug, >> Thank you for your e-mail. Please find attached our command line. >> We felt that the first two lines of code should essentially yield the >> same timing of events. In the first we included the fixed duration of the >> fix (1.0) in our event duration (4.0) and meant to ask for extra null >> events of a minimum duration of 0.0 sec. In the second, we did not include >> the fixed duration of the fix in our event duration (4.0) and meant to ask >> for this by inserting null events of at least 1.0 sec. >> Since the second line of code yielded an error, we run the third line. >> Is this helpful? >> Best, >> Laura >> >> 2013/6/5 Douglas N Greve <gr...@nmr.mgh.harvard.edu <mailto: >> gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>> >> >> >> Hi Laura, what is your command line? >> doug >> >> On 06/04/2013 09:02 AM, Laura Dekkers wrote: >> > >> > Dear Dr Greve, >> > >> > Together with Dr Hilde Huizenga I am implementing an fMRI study in >> > which we would like to optimize the design by using Optseq2. We >> have a >> > few questions. Could you please help us out? >> > >> > Our task consists of 3 runs of 72 trails each, in which participants >> > are presented with a fixation cross that remains on the screen for a >> > fixed duration of 1 sec, followed by one out of nine different >> stimuli >> > that remains on the screen for a fixed duration of 4 sec. >> > This gives a scan duration of 360 sec. We would then like to add 25% >> > jitter, which results in a scan duration of 450 sec, and as TR = >> 2.0, >> > this results in 225 time points. >> > However, Optseq yields an error if ntp is set to 225, ev >> duration set >> > to 4.0, psdwin dPSD to 1.0 , tnullmin to 1.0 and tnullmax to 6.0 >> > ERROR: could not enforce tNullMax=6 (ntries=100000) >> > You will need to reduce the number of time points >> > or increase the number of presentations. >> > However, reducing the number of time points makes Optseq to only >> > insert null events of 1.0 or rarely 2.0 sec without much variation. >> > Optimization with ntp set to 225, ev duration set to 5.0 (=fixed >> > duration of fix + stimulus), psdwin dPSD to 1.0 , tnullmin to >> 0.0 (1.0 >> > does not work) and tnullmax to 6.0 does work. However, this renders >> > Optseq to insert null events of a fixed duration op 1.0 sec, >> which is >> > not what we want. >> > Could you please advise us in how to set these parameters? >> > Thank you in advance. >> > Best regards, >> > Laura Dekkers >> > >> > -- >> > Laura M.S. Dekkers, MSc >> > Research assistant >> > University of Amsterdam - Department of Developmental Psychology >> > Weesperplein 4 >> > 1018 XA Amsterdam - The Netherlands >> > E-mail: lmsdekk...@gmail.com <mailto:lmsdekk...@gmail.com> >> <mailto:lmsdekk...@gmail.com <mailto:lmsdekk...@gmail.com>> >> >> > >> > >> > ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> >> >> >> > >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<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> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<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> >> >> <http://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/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.** >> harvard.edu <Freesurfer@nmr.mgh.harvard.edu>> >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >> >> >> >> >> -- >> Laura M.S. Dekkers, MSc >> Research assistant >> University of Amsterdam - Department of Developmental Psychology >> Weesperplein 4 >> 1018 XA Amsterdam - The Netherlands >> E-mail: lmsdekk...@gmail.com <mailto:lmsdekk...@gmail.com> >> > > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > https://gate.nmr.mgh.harvard.**edu/filedrop2<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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > -- Laura M.S. Dekkers, MSc Research assistant University of Amsterdam - Department of Developmental Psychology Weesperplein 4 1018 XA Amsterdam - The Netherlands E-mail: lmsdekk...@gmail.com
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