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 <greve@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



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Cesar Echavarria
Brain & Cognitive Science
MIT 2012