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Given the specific question about how variable X correlates with change in FA/MD. I would suggest that you compute the difference images and then use a one-sample t-test of the difference images with your covariates.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Wed, Apr 4, 2012 at 9:52 PM, Gershon Spitz <[log in to unmask]> wrote:
Dear FSL list,


I was wondering whether you would be able to advise me on the correct procedure, such as setup of the design matrix for a paired t-test TBSS analysis. But more importantly, advise me how to setup an analysis where I can regress age, education, or a continuous clinical variable on the change oberved between two time points.

For example, I have 10 participants assessed at two time-points. The first step would to be to see whether indeed there is change in FA (but could also check the eigenvalues, RD, etc...) between the two time-points.

Using the Glm Wizard for paired t-test I used the default matrix and contrasts (based on 10 participants at two time points):

Group   EV1     EV2     EV3     EV4     EV5     EV6     EV7     EV8     EV9     EV10    EV11
       A>B     s1      s2      s3      s4      s5      s6      s7      s8      s9      s10
1       1       1       0       0       0       0       0       0       0       0       0
1       1       0       1       0       0       0       0       0       0       0       0
1       1       0       0       1       0       0       0       0       0       0       0
1       1       0       0       0       1       0       0       0       0       0       0
1       1       0       0       0       0       1       0       0       0       0       0
1       1       0       0       0       0       0       1       0       0       0       0
1       1       0       0       0       0       0       0       1       0       0       0
1       1       0       0       0       0       0       0       0       1       0       0
1       1       0       0       0       0       0       0       0       0       1       0
1       1       0       0       0       0       0       0       0       0       0       1
1       -1      1       0       0       0       0       0       0       0       0       0
1       -1      0       1       0       0       0       0       0       0       0       0
1       -1      0       0       1       0       0       0       0       0       0       0
1       -1      0       0       0       1       0       0       0       0       0       0
1       -1      0       0       0       0       1       0       0       0       0       0
1       -1      0       0       0       0       0       1       0       0       0       0
1       -1      0       0       0       0       0       0       1       0       0       0
1       -1      0       0       0       0       0       0       0       1       0       0
1       -1      0       0       0       0       0       0       0       0       1       0
1       -1      0       0       0       0       0       0       0       0       0       1


Contrasts:
               EV1         EV2 EV3     EV4     EV5     EV6     EV7     EV8     EV9     EV10    EV11
Condition A> B    1         0   0       0       0       0       0       0       0       0       0
Condition B> A   -1         0   0       0       0       0       0       0       0       0       0



This matrix and contrast setup was used with this randomise statement:

randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -n 1000 --T2 -V


So firstly, have I set up the matrix, contrast, and randomise statement correctly for this analysis. That is, comparing time1 vs time 2 on FA?


Secondly, and perhaps the more complex analysis, I am trying to then see whether the change between time 1 and time 2 is associated with change on clinical measures over the same time-points.

What is the best way to get TBSS to correlate the change FA values with the change in clinical measures?

Thank you in advance for any assistance that you are able to provide me.

Regards,
Gershon.