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> 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>> 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>>> 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.

                ---------- Forwarded message ----------
                From: *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>>>>
                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>>
        <mailto:wmcgarry@gmu.edu <mailto:wmcgarry@gmu.edu>
        <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
        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>>>
                Phone Number: 617-724-2358 <tel:617-724-2358>
        <tel:617-724-2358 <tel:617-724-2358>>
        <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
        <tel:617-724-2358>>>
                Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
        <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422>

        <tel:617-726-7422 <tel:617-726-7422>>>


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




                The information in this e-mail is intended only for
        the person
                to whom it is
                addressed. If you believe this e-mail was sent to you
        in error
                and the e-mail
                contains patient information, please contact the Partners
                Compliance HelpLine at
        http://www.partners.org/complianceline . If the e-mail was
                sent to you in error
                but does not contain patient information, please
        contact the
                sender and properly
                dispose of the e-mail.




                --            -Ryan


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

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




        --            -Ryan


    --     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>
    Fax: 617-726-7422 <tel:617-726-7422>

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




--
   -Ryan

--
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




--
   -Ryan