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? 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? 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 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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