I want to do the analysis in native space. I saw in a past thread that the native space analysis cannot make use of the -per-run flag. Does this still hold?
If so, is there another way to get fsig.nii file after analyzing each session separately in native space?

Thanks for your help!

Cesar


On Thu, Dec 5, 2013 at 10:16 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

To get the F test, you will need to put the runs from both sessions in the same bold folder (and make sure to use -per-run registration)
doug





On 12/5/13 4:42 PM, Cesar Echavarria wrote:
Thanks for your help Doug. That cleared things up.

One more question, I want to average over 2 of these scan sessions for the same subject. Is there a command or option that will let me do this and output the fsig.nii file for the average activity?

Cesar


On Wed, Dec 4, 2013 at 1:03 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

sorry, there should be an fsig.nii.gz which is the F test of the real and imaginary. That sounds like what you are asking for


On 12/04/2013 12:19 PM, Cesar Echavarria wrote:
To clarify, I am piggy-backing on the retinotopic analysis to map out orientation preference with the travelling-wave method. We presented subjects with a rotating grating and right now I am simply interested in finding the voxels that have significant activity in response to any orientation. Now, when I load the sig.nii file under the 'polar' folder with MATLAB I see that each voxel has 2 values. I understand that these are the p-values for the real and imaginary components of the signal. Is there a way to put these 2 values together for my purposes? Is there a file somewhere in the pipeline that will give me the values I am looking for?

Thanks you for your help

Cesar


On Wed, Dec 4, 2013 at 10:14 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:


    They are compared against 0 (ie, no change from baseline). The
    negatives just mean that the real component was negative
    doug



    On 12/03/2013 06:21 PM, Cesar Echavarria wrote:


        So I want to figure out which voxels were modulated
        significantly by the orientation of our stimuli. Is this the
        right file to look at? If so what are the real and imaginary
        components compared against? I want to know to make sense of
        the negative values.

        On Dec 3, 2013 5:52 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:

              It is the -log10(pvalue) where pvalue is the p-value
        from the F-test
            of the real and imaginary components
            doug





            On 12/03/2013 05:41 PM, Cesar Echavarria wrote:
            > Hi freesurfers,
            >
            > I conducted a retinotopic analysis for one of my
        subjects. I was
            > wondering if any of you knew what is represented by the
        values
            in the
            > sig.nii file under the 'polar' directory that the
        process puts out.
            >
            > I appreciate your help!
            >
            > Cesar
            >
            >
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Cesar Echavarria
Research Assistant
Martinos Center for Biomedical Imaging, Harvard-MGH
Brain & Cognitive Sciences | MIT 2012



--
Cesar Echavarria
Research Assistant
Martinos Center for Biomedical Imaging, Harvard-MGH
Brain & Cognitive Sciences | MIT 2012




--
Cesar Echavarria
Research Assistant
Martinos Center for Biomedical Imaging, Harvard-MGH
Brain & Cognitive Sciences | MIT 2012