Hi Cesar, you cannot really do the analysis you want to do, it is mathematically impossible. If you do not expect a response from one of the conditions, then you could code it as 0. Alternatively, you can consider both conditions as a single 20 sec event and get the FIR for that event out to 28 sec. If you don't have to have an FIR analysis, you can assume a shape to the HRF and do the usual statistics on it. doug
On 03/05/2013 01:21 PM, Cesar Echavarria wrote: > Does the post-stimulus period have to be as long as 12 seconds? With > such a long time window I get the following error when running > selxavg3-sess: > > XCond = 1.47995e+18 (normalized) > ERROR: design is ill-conditioned > > To clarify: in our design we have 10 seconds of condition 1 followed > immediately after with 10 seconds of condition 2 followed by 10 > seconds of fixation. > Given, this what would be the limit on how much post-stimulus time we > should include in our time window? > > Thanks again, > Cesar > > > On Tue, Mar 5, 2013 at 1:00 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > If you presented the stimulus for 10sec, then you should set the > time window to include about 12 sec after stimulus offset. If your > stimulus is 10 secand you want the time window to start 4 sec > prior to onset and go 12 sec after onset, then you will need a > time window of 4+10+12=26sec, so it would be --fir 4 22. You have > to model the return to baseline even if you are not interested > init. Try that and get back to me if it does not work. > doug > > > On 03/05/2013 12:43 PM, Cesar Echavarria wrote: > > Hi Doug, > > As you can see from the attached image (time course on x-axis, > normalized BOLD response on y-axis) the signal peak occurs > earlier than expected if I were to consider the first frame to > be -4 sec relative to stimulus onset. > In our experiment we presented a stimulus for 10 seconds, and > we wanted to see the time course of the BOLD response while > the stimulus was on. We also wanted to see the response of the > aftereffect due to the stimulus separately which is why we are > interested only in the 10 seconds the stimulus is on. > > Thanks, > > Cesar > > > On Tue, Mar 5, 2013 at 12:27 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 Cesar, for your case, it would correspond to 4sec prior to > stimulus onset (the TR that goes from -4 to -3 sec). What > seems to > be wrong? The last frame would be the TR that goes from > +9sec to > +10 sec. Not related to your question, but Is 10 sec post > stimulus > long enough? > doug > > > > On 03/05/2013 11:53 AM, Cesar E Echavarria wrote: > > > Hi Freesurfers, > > I did an FIR analysis to get the BOLD response over > time, the > following way > > mkanalysis-sess -analysis Afterimage_FIR2.rh -surface > self rh > -native > -fwhm 5 -paradigm ShapeAE_New.par -event-related > -polyfit 1 > -mcextreg -TR > 1.000 -nconditions 8 -force -fsd bold -fir 4 14 > > I then generated the relevant contrasts, ran the > funcroi-config command, > and the func-roi-table-sess command to create 14 files > for my > ROI, each > containing the signal value at 14 different time points. > > i.e. > funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c > condition1 > -map cespct > -o ROI/frame0 -frame 0 > > funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c > condition1 > -map cespct > -o ROI/frame1 -frame 1 > > . > . > . > funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c > condition1 > -map cespct > -o ROI/frame13 -frame 13 > > > > My question is this: > > To what time point (relative to stimulus onset) does > the value > in the > frame0 file correspond? > > As I understand it, the first 4 frame values should > correspond > to activity > pre-stimulus. However, this expectation is not > corroborated by > the timing > and pattern of the BOLD response I am observing. > > I would appreciate any guidance on this issue. > > Thanks, > > Cesar Echavarria > > > > -- 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> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > 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. > > > > > -- > Cesar Echavarria > Brain & Cognitive Science > MIT 2012 > > > -- > 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> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > -- > Cesar Echavarria > Brain & Cognitive Science > MIT 2012 -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
