Dear Doug, Thank you for your explanations and suggestions. I tested the code under the new Optseq version and it seems to generate proper output now.
Thanks a lot! Best regards, Laura 2013/6/21 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > > On 6/20/13 5:55 AM, Laura Dekkers wrote: > > Dear Doug, > > Thank you for your e-mail. > As you suggested, we changed tnullmax to 6 sec and run the following code in > Optseq: > --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 7.0 --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_test5 > > Although, this yielded no errors, I have several questions as to whether we > got the results we actually wanted to. > > First, we repeatedly got a matrix rank-deficient message, like: > /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: > vnl_qr<T>::solve() : matrix is rank-deficient by 94 > I am not sure whether this of a fundamental problem. Could you please give > your opinion on that? > > Not necessarily a problem. optseq tries lots of designs, and it does not > know that they are bad until it tries to invert them. It is not a problem > unless all of them are like that. It would be better to not print that > error, but it is in some 3rd party code, and I don't have control over it. > > > Second, you advised u to change tnullmax from 6 to 7 sec in the above code, > so that it would be a mathematically equivant of the code below. > --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 > > However, we are not sure why this would be true. Could you please help to > explain this? > > In the original cmd (tnullmin=0, max=6, stim=5), the stim is 4s stim + 1s > hidden null. With a tnullmax=6, it means that you could have a null that was > as long as 1+6=7s long (but least 1s long). In the new cmd, stim=4, min=1, > max=7, which explicitly does the same thing. > > > > Finally, we originally wanted null events of at maximum 6 sec. You then > advised us to change tnullmax from 6 to 7 sec. However, this does not > restrict Optseq to insert null events of 7 sec at maximum. We occationally > found Optseq to insert null events of 8 sec. Furthermore, the last null > event Optseq inserts, allways is of a 12 sec duration. Do you have any idea > why this is the case and hou we could change this? > > I might have fixed this. Try using this version > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2 > > let me know if you still have a problem. > doug > > > I am aware that I am posting a lot of questions at once. I hope you can find > the possibility and time to help us out. > Thank you in advance. > > Best, > Laura > > > > 2013/6/15 Douglas Greve <gr...@nmr.mgh.harvard.edu> >> >> >> Hi Donna, on the 2nd command line you need to change --tnullmax to 7 sec >> to be compatible with the 1st command line. I ran this and it works. >> doug >> >> >> >> >> On 6/11/13 8:45 AM, Laura Dekkers wrote: >> >> 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>> >>>> >>>> >>>> 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:Freesurfer@nmr.mgh.harvard.edu> >>>> >>>> > 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> >>>> 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. >>>> >>>> >>>> >>>> >>>> -- >>>> 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 >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: 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 >> >> >> > > > > -- > 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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