can you send the fsgd file and command line?

On 10/30/2012 06:42 PM, Ryan wrote:

Doug, Also, I tried running this analysis but got the error below. This makes me think it's because of all of the 1's and -1's in my FSGD file, should I just have a factor called "Training" with a "yes" or a "no" for each subject?

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.

On Tue, Oct 30, 2012 at 5:57 PM, Ryan <wmcgarry@gmu.edu mailto:wmcgarry@gmu.edu> wrote:

Doug,
   So if I wanted to test if there were effects of training
compared to the control condition, and I had 4 subjects (2 per
group), would the format for my two files shown below be correct?
Thanks.


FSGD file:
GroupDescriptorFile 1
Class Subject1
Class Subject2
Class Subject3
Class Subject4
Variables TP1-vs-TP2.Group1TrainTP1-vs-TP2.Group2Control
Input 1-2_recon   Subject11                        0
Input 1-3_recon   Subject11                        0
Input 2-2_recon   Subject21                        0
Input 2-3_recon   Subject21                        0
Input 3-1_recon   Subject3        0-1
Input 3-2_recon   Subject3 0-1
Input 4-1_recon   Subject4        0-1
Input 4-2_recon   Subject40-1


Mtx file:
0 0 0 0 1 0
0 0 0 0 0 -1

Additional Mtx file examining cortical thinning or thickening in
the training group:
0 0 0 0 1 0


On Tue, Oct 30, 2012 at 4:44 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    See http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
    This is for a single group. For two groups with 3 time points.
    In your case, you only have 2 time points (so no TP1-vs-TP3
    variable). To account for the 2nd group, create two variables:
    TP1-vs-TP2.Group1 and TP1-vs-TP2.Group2. If a subject is in
    Group1, then set the Group2 variable to 0.
    doug


    On 10/30/2012 04:38 PM, Maren Strenziok wrote:

        If you don't agree with our matrix and contrasts, can you
        please send us a matrix example for a 2x2 within and
        between subjects ANOVA model and contrasts to get the
        interaction effect?
        Maren

        On Oct 30, 2012, at 4:22 PM, Douglas N
        Greve<greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>>  wrote:

            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><mailto: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>>
                <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:

                            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>>>
                <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
                <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>>>
                <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
                <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>
                <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
                <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>>>
                <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
                <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><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
                <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
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                <mailto:greve@nmr.mgh.harvard.edu>
                <mailto:greve@nmr.mgh.harvard.edu
                <mailto:greve@nmr.mgh.harvard.edu>>>>>
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                            --     Douglas N. Greve, Ph.D.
                            MGH-NMR Center
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                    --     Douglas N. Greve, Ph.D.
                    MGH-NMR Center
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                -- 
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            -- 
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    -- 
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    MGH-NMR Center
    greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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-- -Ryan