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.eduwrote:
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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/**compliancelinehttp://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.