Re: [Freesurfer] Files

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