Re: [Freesurfer] Files

Hi Ryan, I don't understand your model. This does not look like a standard repeated measures ANOVA. Is it supposed to be equivalent? doug

On 10/30/2012 02:07 PM, Ryan wrote:

Doug, Just so our study is understandable, subjects completed a 6 week period of training or no training (i.e. the control condition) with a scan at the beginning and end of the period. Thus, I entered the pre and post-scans for training and control subjects in the input files. The names for all the subjects are kept in an ordered list, referenced by the other two files I describe below. In the Xg.dat file, the first column has a +1 for each control subject's pre-scan and a -1 for each control subject's post-scan. The second column has a +1 for each training subject's pre-scan and a -1 for each training subject's post-scan. The remaining columns each pertain to a specific subject's two scans, with 1's showing FreeSurfer which two scans are being compared pre to post. In the mtx file, the -1 references the first column in Xg.dat (control subjects) and the +1 references the second column in Xg.dat (training subjects). The remaining 0's refer to the other subjects or columns in Xg.dat. So in order to determine whether there's thickening or thinning in the controls and training subjects, would I still need to use an additional analysis with the contrasts [1 0 0 ....] and [0 1 0 ....]? Thank you.

On Tue, Oct 30, 2012 at 11:28 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Hi Ryan, I'm a little lost here. Can you resend your X and
contrast matrices and explain what each column is?
doug


On 10/26/2012 03:45 PM, Ryan wrote:

    Doug,
       Actually my input is not the difference map, but the
    separate time points (it's timepoint 2 weighted with -1 and
    timepoint 1 weighted with 1, described in the matrix file I
    sent you). So in order to determine whether there's thickening
    or thinning in the controls and training subjects, would I
    still need to use the additional contrasts [1 0 0 ....] and [0
    1 0 ....]? Thank you.

    On Thu, Oct 25, 2012 at 3:48 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:

        And the input is already TimePoint2-TimePoint1? If so,
    then you
        will need two more contrasts: [1 0 0 ....] and [0 1 0
    ....]. The
        first tells you if controls are thinning (blue) or thickening
        (red), the 2nd tells you if the training is doing the same.
        doug


        On 10/25/2012 03:34 PM, Ryan wrote:

            Doug,
               Yes, it's a longitudinal study since we MRI
    participants
            pre-training and post-training.

            On Thu, Oct 25, 2012 at 2:37 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>>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>

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

                I'm not sure I understand. Is this a longitudinal
    study?


                On 10/25/2012 01:26 PM, Ryan wrote:

                    Doug,
                       Also, how can I tell if it's thickening or
    thinning if
                    red/blue corresponds to the group? Thanks for
    the help.

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                    Date: Thu, Oct 25, 2012 at 12:20 PM
                    Subject: Re: Files
                    To: Ryan <wmcgarry@gmu.edu
    <mailto:wmcgarry@gmu.edu> <mailto:wmcgarry@gmu.edu
    <mailto:wmcgarry@gmu.edu>>
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    <mailto:wmcgarry@gmu.edu <mailto:wmcgarry@gmu.edu>>
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    <mailto:wmcgarry@gmu.edu <mailto:wmcgarry@gmu.edu>>>>>


                    That contrast will compute training-controls.
    In the maps,
                    red/yellow will mean training>controls, blue/cyan
            otherwise

                    doug



                    On 10/25/2012 12:47 AM, Ryan wrote:

                        Doug,
                           Here are the Xg.dat (where the first
    column is for
                    controls and
                        the second column is for training
    subjects) and
            mtx files, I
                        didn't use the FSGD design. Please let me
    know if
            this is
                        sufficient for you to answer my question,
    thank
            you very much.

                        --        -Ryan


                    --         Douglas N. Greve, Ph.D.
                    MGH-NMR Center
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            --            -Ryan


        --     Douglas N. Greve, Ph.D.
        MGH-NMR Center
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    -- 
       -Ryan


-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
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Phone Number: 617-724-2358 <tel:617-724-2358>
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-- -Ryan