Hi fsl users,
I have a tbss dataset with a control group, a patient group, and 4 timepoints for each subject. I am trying to create a GLM design that essentially models a 2x4 ANOVA with 1 repeated measure (time). I was hoping that anyone who has worked with a similar design could look over my setup and steer me in the right direction. This study has 11 controls and 21 patients, but for simplicity, the following design has 3 controls and 4 patients. I would appreciate any corrections or better approaches to the design below:
.mat file:
cont1_T1 1 0 0 0 0 0 1 0 0 0 0 0 0
cont1_T2 0 1 0 0 0 0 1 0 0 0 0 0 0
cont1_T3 0 0 1 0 0 0 1 0 0 0 0 0 0
cont1_T4 0 0 0 0 0 0 1 0 0 0 0 0 0
cont2_T1 1 0 0 0 0 0 0 1 0 0 0 0 0
cont2_T2 0 1 0 0 0 0 0 1 0 0 0 0 0
cont2_T3 0 0 1 0 0 0 0 1 0 0 0 0 0
cont2_T4 0 0 0 0 0 0 0 1 0 0 0 0 0
cont3_T1 1 0 0 0 0 0 0 0 1 0 0 0 0
cont3_T2 0 1 0 0 0 0 0 0 1 0 0 0 0
cont3_T3 0 0 1 0 0 0 0 0 1 0 0 0 0
cont3_T4 0 0 0 0 0 0 0 0 1 0 0 0 0
pat1_T1 0 0 0 1 0 0 0 0 0 1 0 0 0
pat1_T2 0 0 0 0 1 0 0 0 0 1 0 0 0
pat1_T3 0 0 0 0 0 1 0 0 0 1 0 0 0
pat1_T4 0 0 0 0 0 0 0 0 0 1 0 0 0
pat2_T1 0 0 0 1 0 0 0 0 0 0 1 0 0
pat2_T2 0 0 0 0 1 0 0 0 0 0 1 0 0
pat2_T3 0 0 0 0 0 1 0 0 0 0 1 0 0
pat2_T4 0 0 0 0 0 0 0 0 0 0 1 0 0
pat3_T1 0 0 0 1 0 0 0 0 0 0 0 1 0
pat3_T2 0 0 0 0 1 0 0 0 0 0 0 1 0
pat3_T3 0 0 0 0 0 1 0 0 0 0 0 1 0
pat3_T4 0 0 0 0 0 0 0 0 0 0 0 1 0
pat4_T1 0 0 0 1 0 0 0 0 0 0 0 0 1
pat4_T2 0 0 0 0 1 0 0 0 0 0 0 0 1
pat4_T3 0 0 0 0 0 1 0 0 0 0 0 0 1
pat4_T4 0 0 0 0 0 0 0 0 0 0 0 0 1
EVs 1-3 model controls at each timepoint, 4-6 model patients at each timepoint, and 7-13 model the individual subject means.
contrasts:
Controls-Patients: 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 X Ftest1: Main effect of Group
Time1-Time4: 1 0 0 1 0 0 0 0 0 0 0 0 0 X
Time2-Time4: 0 1 0 0 1 0 0 0 0 0 0 0 0 X Ftest2: Main effect of Time
Time3-Time4: 0 0 1 0 0 1 0 0 0 0 0 0 0 X
C(T1-T4)-P(T1-T4): 1 0 0 -1 0 0 0 0 0 0 0 0 0 X
C(T2-T4)-P(T2-T4): 0 1 0 0 -1 0 0 0 0 0 0 0 0 X Ftest3: Interaction Group x Time
C(T3-T4)-P(T3-T4): 0 0 1 0 0 -1 0 0 0 0 0 0 0 X
And I can also include contrasts for T1-T3, T2-T3, T1-T2, C(T1-T3)-P(T1-T3), C(T2-T3)-P(T2-T3), C(T1-T2)-P(T1-T2), but not include them as ftests right? (since they are linear combinations of the others)
I am not sure how the data should be grouped for the exchangability blocks, so I have them all in one group in the .grp file, is that correct?
Does this setup look appropriate?
attached are the graphical representations.
thanks for the help,
Kyle Kern
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of MCLAREN, Donald [[log in to unmask]]
Sent: Wednesday, March 18, 2009 10:06 PM
To: [log in to unmask]
Subject: Re: [FSL] modeling slope over time
Instead of estimating the within-subject slopes, I'd do a repeated measures ANOVA. In the ANOVA, you will want subject, group, time, and a group-by-time interaction term. The reason for doing it this way is to avoid the assumption that the change is linear with time.
On Wed, Mar 18, 2009 at 10:01 PM, Kyle Kern <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi,
I am trying to set up a longitudinal tbss analysis over 4 time points contrasting a patient
group to a control group. I'm interested in change over time rather than the effect of any
specifc time point. I was planning to model the slope for each subject and then put this
into a group t-test. Would modelling the slope for each subject be the same approach as a
simple correlation where my design matrix might look like this?:
-3
-1
1
3
Would this reflect the magnitude of the slope or does it only reflect the linearity like a
correlation coefficient? I would hypothesize that patients show a steeper slope than
controls though they may show more variability, so a least squares regression slope
might detect differences but a simple correlation coefficient might not.
Also, to perform a 2 level analysis with tbss is it preferable to use randomise and feed
the within subject t-stat into the group comparison or should I use the feat gui and treat
each within subject analysis as a timeseries and feed that into a higher level mixed
effects analysis?
thanks for all the help,
Kyle Kern
--
Best Regards, Donald McLaren
=====================
D.G. McLaren
University of Wisconsin - Madison
Neuroscience Training Program
Office: (608) 265-9672
Lab: (608) 256-1901 ext 12914
=====================
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