On Tue, Oct 30, 2012 at 6:03 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Not quite, changes to FSGD file below as well as comments on the contrast matrix

On 10/30/2012 05:57 PM, Ryan 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 Subject1+1 0
Input 1-3_recon Subject1-1 0
Input 2-2_recon Subject2+1 0
Input 2-3_recon Subject2-1 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

This matrix would find places where either Group1 OR Group2 changed between time points. I think you want to know if there is a difference in the change between groups. For this, you would have [0 0 0 0 1 -1].

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

Correct

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>>
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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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<mailto: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>>>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto: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>>>
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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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<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
<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>>>
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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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<mailto: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
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<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>>>>>
Phone Number: 617-724-2358
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<tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358>
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<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><tel:617-726-7422

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

<tel:617-726-7422 <tel:617-726-7422>>
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<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>
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The information in this e-mail
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-- -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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Phone Number: 617-724-2358
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<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><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>
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-- -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
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<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
Phone Number: 617-724-2358
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<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:
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-- -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
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Bugs:
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FileDrop:
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-- -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
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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

-- 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>
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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<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