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Hi,
     It looks like the scan order matches the design - it might be worth visually inspecting the input files as corrupted data could produce the same problem..

Many Regards

Matthew 

Hello Matthew,

The scans are alphabetically titled as:

End_subjectA
End_subjectB
End_subjectC
End_subjectD
Pre_subjectA
Pre_subjectB
Pre_subjectC
Pre_subjectD

which I believe matches my design matrix.  

You are right, randomise is still executing but with no further output for hours!

Chris

On Fri, Sep 24, 2010 at 5:50 AM, Matthew Webster <[log in to unmask]> wrote:
Hello,
           This error usually comes from a problem with the design ( such as mismatch between it and the data ). Can you check that the order of the scans in your input data matches the order specified in the design? Also is the randomise process actually terminating after the "integral steps" message or is it still executing ( it should continue the integration, although no further output will be written to the screen )?

Many Regards

Matthew


Hello friends of FSL,

I am trying to run a pairwise analysis of effect over an intervention, using 4 subjects, each with one scan before intervention and one scan after intervention. However, randomise is quitting after 5 permutations with the "large number of integral steps" error below. This is FSL 4.1.6.  Is there an error in my design matrix? (Made with Glm). It is only a problem with using the --T2 option.

Thank you,
Chris Chapman
University of Michigan Medical School
-----
randomise options: -i all_FA_skeletonised -o TBSS_PAIRWISE -d pairwise.mat -t pairwise.con -m mean_FA_skeleton_mask --T2 -V --debug
Loading Data:
Data loaded
Confounds detected.
Subject | Design | group | label
1.000000 1.000000 1.000000 1.000000
2.000000 1.000000 1.000000 1.000000
3.000000 1.000000 1.000000 1.000000
4.000000 1.000000 1.000000 1.000000
5.000000 -1.000000 1.000000 2.000000
6.000000 -1.000000 1.000000 2.000000
7.000000 -1.000000 1.000000 2.000000
8.000000 -1.000000 1.000000 2.000000

70 permutations required for exhaustive test of t-test 1
Input Design:
1.000000 -1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 -1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 -1.000000 0.000000
1.000000 0.000000 0.000000 0.000000 -1.000000
-1.000000 -1.000000 -0.000000 -0.000000 -0.000000
-1.000000 -0.000000 -1.000000 -0.000000 -0.000000
-1.000000 -0.000000 -0.000000 -1.000000 -0.000000
-1.000000 -0.000000 -0.000000 -0.000000 -1.000000

Input Contrast:
1.000000 0.000000 0.000000 0.000000 0.000000

Contrast rank: 1
Dof: 3 original dof: 3
Doing all 70 unique permutations
Starting permutation 1 (Unpermuted data)
statistic Maximum: 49.67
Starting permutation 2
statistic Maximum: 1.73205
Starting permutation 3
statistic Maximum: 28.6022
Starting permutation 4
statistic Maximum: 2.99991
Starting permutation 5
statistic Maximum: 9.41493e+14
Warning: tfce has detected a large number of integral steps. This operation may require a great deal of time to complete.

-----

view pairwise.mat
/NumWaves       5
/NumPoints      8
/PPheights              2.000000e+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
1.000000e+00    0.000000e+00    1.000000e+00    0.000000e+00    0.000000e+00
1.000000e+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    1.000000e+00
-1.000000e+00   1.000000e+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
-1.000000e+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    1.000000e+00

-----

view pairwise.con
/ContrastName1   "A > B"
/ContrastName2   "B > A"
/NumWaves       5
/NumContrasts   2
/PPheights              2.000000e+00    2.000000e+00
/RequiredEffect         124.604 124.604

/Matrix
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


--
Christopher H. Chapman
[log in to unmask]
[log in to unmask]




--
Christopher H. Chapman
[log in to unmask]
[log in to unmask]