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design.con:

/NumWaves 4
/NumContrasts 2
/PPheights 1 1
/Matrix
1 -1 0 0
-1 1 0 0

design.mat:

/NumWaves 4
/NumPoints 43
/PPheights 1 1
/Matrix
0 0 32.48549 2
0 0 41.22221 2
0 0 22.02935 2
0 0 22.31409 2
0 0 21.62688 2
0 0 20.55635 2
0 0 29.85434 2
0 0 27.22046 1
0 0 18.80407 1
0 0 34.81273 1
0 0 24.07732 2
0 0 22.6536 1
0 0 19.62819 2
0 0 26.24302 1
0 0 18.05388 2
0 0 42.10382 2
0 0 26.50312 1
0 0 24.39766 2
0 0 31.75172 1
0 0 18.56314 1
0 0 25.58592 2
0 0 29.91458 2
0 0 29.649 2
0 0 22.87263 1
1 0 34.35275 2
0 1 23.47771 2
1 0 25.82412 1
0 0 20.38933 2
1 0 26.13624 1
0 1 25.38879 1
0 1 22.92739 1
1 0 21.6789 2
0 0 50.45723 2
1 0 20.24149 2
1 0 20.89037 1
0 1 18.28387 1
0 1 25.74745 1
1 0 22.22922 1
1 0 36.23371 2
0 1 18.70003 1
1 0 44.25583 2
0 1 43.9793 2
1 0 41.87384 2

What is the output from randomise - does it appear to be "stuck" on a particular permutation - e.g. "Starting permutation <x>"? Can you let us know the contents of your design.mat and design.con?

Matthew

Hi, FSL experts

I am trying to do some ROI analysis on 20 subjects. I manually drew a mask and used fslmaths to create the final mask according to mean_FA_skeleton_mask. Then I ran

randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -n 500 -T

It has been a week and it seems it is still running.

My computer info:

Memory: 7.8 GB
Processor 0: Intel Xeon CPU E5345 @ 2.33 GHZ
Processor 1: Intel Xeon CPU E5345 @ 2.33 GHZ
Processor 2: Intel Xeon CPU E5345 @ 2.33 GHZ
Processor 3: Intel Xeon CPU E5345 @ 2.33 GHZ
Processor 4: Intel Xeon CPU E5345 @ 2.33 GHZ

So is this normal? How long should it take?

Many thanks!
Bai

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