Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

You don't generate a negative coefficient. The sign and magnitude of the coefficient is determined by the fitting procedure. It may be the case that a positive coef fits the data better than a negative. You should not change the gamma parameters. doug

On 04/24/2013 04:06 PM, SHAHIN NASR wrote:

I know but how can we generate negative coefficient? To clarify, we use alpha=2, delta=2.25 tau=1.25 to generate default HRF. Using negative values for alpha, delta or tau, does not invert the shape of the curve (HRF).

On Wed, Apr 24, 2013 at 3:12 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

What do you mean the gamma function generates positive values? It
will create a regressor with a positive-going HRF. However, the
regression coefficient can be negative which would invert the
shape. The reg coef is fit to the data, so the data will tell you
whether there is an undershoot or not.
doug



On 04/24/2013 03:02 PM, SHAHIN NASR wrote:

    Hi Doug,
        Sorry to follow this topic with a delay but we tried to
    model BOLD signal undershoot with a gamma function and we
    failed. The problem is, gamma function generates positive
    values and we can NOT use "inverse gamma function" (or
    otherfunction similar to that) as a part of mkanalysis-sess
    (for modeling BOLD signal undershoot). We even used matlab
    gammafit to estimate parameters and it said that values should
    be positive otherwise gammafit function fails.
        Do you have any suggestion?



    On Wed, Apr 10, 2013 at 6:46 PM, Douglas N Greve
    <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>> wrote:


        yes, that is what you want. The only other way that comes
    to mind
        is to model each event type as two event types one delayed
        relative to the other. Then model the responseto each as a
    gamma.
        If the delay is right, then the first gamma should model
    the main
        positive response and the second gamma will model the negative
        response. both will be independent from the other.

        doug


        On 04/10/2013 05:00 PM, shahin@nmr.mgh.harvard.edu
    <mailto:shahin@nmr.mgh.harvard.edu>
        <mailto:shahin@nmr.mgh.harvard.edu
    <mailto:shahin@nmr.mgh.harvard.edu>> wrote:

            I think I figured it out but I want to double check. I am
            generating
            group-average map for my subjects using isxconcat-sess
    command
            which
            generates ces maps for each time frame. I think these
    maps are
            what I
            wanted. Right?
                If you still have other solutions that you think may
            generate more
            reliable results, I am eager to know. For instance, is
    there
            anyway to
            fit a model as we do for spmhrf or fslhrf, but just
    for the
            negative
            peak?

            Regards

                That's the problem Doug. I have already generated
    the FIR
                model but how
                can
                I show the sig MAP for one "particulat time
    point".  What
                are the other
                ways?


                On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
                <greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>
                <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>>wrote:


                    Hi Shahin, there are several ways that you
    could do
                    it. The one that
                    immediately comes to mind is to use an FIR and
    then
                    test for a
                    difference
                    at a particular post stimulus time point.
                    doug




                    On 04/10/2013 03:54 PM, SHAHIN NASR wrote:

                        Hi,
                              I want to generate a map to show the
                        significant difference
                        between
                        HRF undershoot  (negative peak of activity)
                        between two conditions
                        independent from the positive peak. Is there
                        anyway, to generate this
                        map?

                        P.S.: Please note that I need a map and
    not a time
                        course graph.


                        --
                        Shahin Nasr

                        PhD in Cognitive Neuroscience
                        Martinos Imaging Center, MGH
                        Harvard Medical School

                    --
                    Douglas N. Greve, Ph.D.
                    MGH-NMR Center
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                    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
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                --
                Shahin Nasr

                PhD in Cognitive Neuroscience
                Martinos Imaging Center, MGH
                Harvard Medical School



                --
                Shahin Nasr

                PhD in Cognitive Neuroscience
                Martinos Imaging Center, MGH
                Harvard Medical School
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    -- 
    Shahin Nasr

    PhD in Cognitive Neuroscience
    Martinos Imaging Center, MGH
    Harvard Medical School


-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
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-- Shahin Nasr

PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School