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Hi Brigitte,

I don't really understand what you mean by "struct-behav" analysis and how that would differ from the "struct" analysis. Also I don't understand what you mean by the "this" in your first paragraph (see highlighted below). Could you clarify?

Thanks!

All the best,

Anderson

On Thu, 8 Nov 2018 at 07:13, Brigitte Evers <[log in to unmask]> wrote:

Dear FSLusers,

I am fairly new to TBSS and would like to check if I am doing the correct thing! I am trying to do a paired t-test to look at structural changes in FA before and after an intervention in 9 lesion patients. I then want to correlate this to performance on an cognition task. I am aware that I have 2 options (1) subtracting FA images post-intervention from pre-intervention with fslmaths (2) create design and contrast files according to FEAT paired t-test manual (we chose for the latter for visualisation purposes)

My question is do I set up the struct-behav analysis matrix file the same as the structural analysis part (e.g. 10 EVs/columns) or do I just create 1 EV/column with cognition data (+additional columns for covariates) with the struct-behav analysis (and how do I know FSL "remembers" the within subjects group design of the structural part)?

Any help you could offer would be highly appreciated!

Best wishes,
Brigitte

For the structural analysis I have created contrast and matrix files according tp the FEAT manual:
/NumWaves 10
/NumPoints 18
/PPheights 2.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00

/Matrix
/NumWaves 10
/NumPoints 18
/PPheights 2.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00

/Matrix
1.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
-1.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
-1.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
-1.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
-1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
-1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
-1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
-1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
-1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
-1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00

/NumWaves 1
/NumPoints 18

/Matrix
1
2
3
4
5
6
7
8
9
1
2
3
4
5
6
7
8
9

/ContrastName1 preint - postint
/ContrastName2 postint - preint
/NumWaves 10
/NumContrasts 2
/PPheights 2.000000e+00 2.000000e+00
/RequiredEffect 5.446 5.446

/Matrix
1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
-1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00

For the functional analysis I am doubting between these 2 contrast matrixes (I used the same .grp file)
(1)
/NumWaves 1
/NumPoints 18
/PPheights 2.000000e+01

/Matrix
1.900000e+01
1.800000e+01
2.000000e+01
1.700000e+01
1.900000e+01
1.900000e+01
1.800000e+01
2.000000e+01
1.600000e+01
5.000000e+00
7.000000e+00
4.000000e+00
7.000000e+00
8.000000e+00
5.000000e+00
7.000000e+00
8.000000e+00
2.000000e+00

(2)
/NumWaves 10
/NumPoints 18
/PPheights 2.000000e+00 5.000000e+00 6.000000e+00 6.000000e+00 6.000000e+00 6.000000e+00 6.000000e+00 6.000000e+00 6.000000e+00 5.000000e+00

/Matrix
1.000000e+00 5.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00 6.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00 0.000000e+00 5.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 6.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 6.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 6.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 6.000000e+00 0.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 4.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 5.000000e+00
-1.000000e+00 4.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
-1.000000e+00 0.000000e+00 6.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
-1.000000e+00 0.000000e+00 0.000000e+00 6.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
-1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 5.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
-1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 6.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
-1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 6.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
-1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 6.000000e+00 0.000000e+00 0.000000e+00
-1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 6.000000e+00 0.000000e+00
-1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 5.000000e+00

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