Sorry, that read gender and age. The contrast takes age into account, it is just a problem with the code that generates the sentence. Have not had a chance to answer the others, I thought I'd try to get one wrapped up. It looks like you added a few more questions at the end. Unless they are closely related to the previous questions, can you send them separately, it is hard to keep track with all the replies to replies. doug

On 05/23/2013 02:51 PM, Tudor Popescu wrote:

Thanks Doug, however my question was why does QDEC not also display a contrast to the effect of "Does the avg thickness, accounting for *gender and age*, differ between group1 and group2?", instead it only displays "Does the avg thickness, accounting for *gender*, differ between group1 and group2?"

Also, I was wondering whether you got a chance to see my other questions from the same email..

Many thanks! Tudor

On 23 May 2013 17:49, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

when I run qdec using your table and my data, I get a full
complement of contrasts, see attached.
doug




On 05/22/2013 01:43 PM, Tudor Popescu wrote:


                >     1) In a design with group and gender as discrete
            factors and age
                >     as a continuous factor, why is it that QDEC only
            displays the
                >     contrast "Does the avg thickness, accounting for
            gender, differ
                >     between group1 and group2?" and not also
            "..acounting for gender
                >     and age,.."?
                >
                I thought that it would have. Are you coding age
    as a nuisance
                variable?
                Also, are you coding gender as a continuous
    variable? That is
                something
                you should not do.


            I was not coding age as a nuisance variable but as a
            continuous variable (co-variate). Gender was a
    discrete/fixed
            factor but I'm not sure whether this means
    'continuous' in the
            sense discussed in your exchange with Arman. Anyway,
    in this
            configuration, it seems gender and age are not accounted
            (controlled) for at the same time.

        It should be. Can you send your qdec table?

    See attached



                >     3) From the group tutorial, I see that
    mris_preproc
            has to be
                >     called with flag "--cache-in
            ess.fwhm10thickn.fsaverage".
                However,
                >     after running recon-all (including with the
    –qcache
            option)
                on all
                >     my subjects, none of their folders contains
    a file named
                >     ?h.thickness.fwhm10.fsaverage.mgh
                >
                Where does it say to use ess.fwhm10thickn.fsaverage?

            Sorry, typo. The flag is actually "--cache-in
            thickness.fwhm10.fsaverage", I file that I do not have
    after
            having run recon-all (including with the --qcache option)

        Try running recon-all again with just the --qcache flag.

    This is what I had done previously; the command was:
    recon-all -s C${i} -qcache
    where the ${i} was a counter in a script, to run the command
    on all my subjects



                >     5) What is the difference between running
                make_average_subject and
                >     running mris_preproc with --target fsaverage?
                >
                make average subject makes the average subject.
    mris_preproc
                samples the
                data into a common space defined by the registration
            surface and
                concatenates the input subjects into a single stack.

            But should the registration surface used by
    mris_preproc (i.e.
            its "--target" flag) come from the 'average' subject
    or from
            'fsaverage'? In other words, which one of these
    becomes the
            study-specific template?

        You have to tell mris_preproc both the target and the surface
        registration to use if you  want to use a different
    average subject.

    The command I used is:

    mris_preproc --fsgd group_gender__age.fsgd --target average
    --hemi rh --meas thickness --out rh.thickness.mgh

    So if I understand correctly, the fact that I didn't indicate
    a surface registration means that the surface from the
    "average" subject will be used, rather than the one from
    "fsaverage"? I still don't understand the difference between
    those two, and which, if any, can be referred to as the
    study-specific template.

            B) All concatenated volumes from mris_preproc's output
    files
            (?h.thickness.mgh) appear blank in freeview, even
    though the
            individual structurals all look fine. Also,
    lh.thickness.mgh
            and rh.thickness.mgh have, surprisingly, *exactly* the
    same
            file size, which is also a bit small (~25MB) to be able to
            contain 38 registered structurals, which suggests
    something
            went wrong...

        These are surface overlay files, not volumes. You can't load
        surfaces as volumes in freeview.

    So assuming I don't visually inspect the surface overlays, can
    I assume that mris_preproc ran fine if lh.thickness.mgh and
    rh.thickness.mgh have exactly the same file size?

            C) When running mri_surf2surf, I get an error saying
    that file
            /surf/lh.white cannot be opened. The 'average' folder
    produced
            after I ran make_average_subject does not contain a
            /surf/lh.white file, only a /surf/lh.white_avg file! I
    didn’t
            find a log file from make_average_subject so i don’t
    know if
            it gave any errors..

        It's extremely helpful to have command lines ...


    Sorry, my commands were:
    make_average_subject --subjects C01 C02 C03 C04 C05 C06 C07
    C08 C09 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 M01 M02 M03
    M04 M05 M06 M07 M08 M09 M10 M11 M12 M13 M14 M15 M16 M17 M18 M19
    mri_surf2surf --hemi lh --s average --sval lh.thickness.mgh
    --fwhm 10 --tval lh.thickness.10.mgh
    _________________________

    Could someone please explain how the following descriptions of
    a contrast are exactly linked:
    i) a contrast's namesake folder (including keywords
    'Avg'/'Diff'/'X' and 'Intercept'/'Cor'; e.g.
    "lh-Diff-group1-group2-Cor-thickness-behaviouralMeasure"),
    ii) its phrasing in QDEC ("Does the thickness-age correlation
    differ between group1 and group2?"),
    iii) the assignment of values to each column of the design
    matrix, in the C.dat contrast vector (e.g. [0, 0, 1, -1])

    _________________________
    (this is actually a bug report) After setting a different FDR
    threshold and pressing the "Set Using FDR" button, more often
    than not the results image doesn’t change accordingly. I
    noticed that the button only has an effect after moving around
    the QDEC window and/or waiting a minute or so


-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422

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