Also, did you mean ' fir 4 26' in your previous response? since the TimeWindow parameter should include the 'PreStimulus' time (I just want to double check since this is crucial to my question)
Cesar On Tue, Mar 5, 2013 at 1:00 PM, Douglas N Greve <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<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<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: >> 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/> >> >> >> >> >> 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. >> >> >> >> >> -- >> 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<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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > -- Cesar Echavarria Brain & Cognitive Science MIT 2012
_______________________________________________ Freesurfer mailing list 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.
