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.Group1Train TP1-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 Subject4 0 -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> 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> 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>> 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.

---------- 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>>>>>
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>>>>>

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>>>
<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>>>>
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>>>
<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<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>>> <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>
<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>
<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>>
<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>

-- -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

--
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