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 <greve@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 <greve@nmr.mgh.harvard.edu <mailto: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



    --     Douglas N. Greve, Ph.D.
    MGH-NMR Center
    greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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    Fax: 617-726-7422 <tel:617-726-7422>

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    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

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    ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/




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--
Cesar Echavarria
Brain & Cognitive Science
MIT 2012

--
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/BugReporting
FileDrop: 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