Hi Alejandro,
so it seems that it might be related to your first permutation, since changing the design matrix helps. I seem to recall something similar happening for one of my datasets, but unfortunately only Matt will be able to help on this matter. Just out of curiosity, does it complete despite the error message or does it stall forever, and what version of FSL are you using?
Cheers,
Gwenaëlle
------------------------------------------------------------------------------------
Gwenaëlle Douaud, PhD
MRC Career Development Fellow
FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington
OX3 9DU Oxford UK
Tel: +44 (0) 1865 222 523
Fax: +44 (0) 1865 222 717
www.fmrib.ox.ac.uk/team/principal-investigators/gwenaelle-douaud-----------------------------------------------------------------------------------
Hi Gwenaëlle,
I tried to use a mask (binarized skeleton of mean FA map ) and the same warning was thrown. Also, I tried to use an incorrect design matrix (5 subjects in group A and 13 in B) for check the data and it worked! Unfortunately it doesn't work with the correct design.
Thanks for your help!
Alex
El 11/07/2013 20:40, "Gwenaëlle DOUAUD" <
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Hi Alejandro,
I am not sure what this error message means and I suspect Matt (Webster) would have a much better clue than me, but in the mean time, I just would like to double-check: have you used a mask in your randomise command? The rest looks ok to me.
Cheers,
Gwenaëlle
Thanks for the suggestion.
-d refers to the next argument, design matrix file. Is that correct?
Cheers,
Alex
El 11/07/2013 20:27, "Rosalia Dacosta Aguayo" <
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Hi,
It is just a suggestion, but have you tried without the -d flag?
Bert regards,
Rosalia.
El 11/07/2013 20:19, "Alejandro" <
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Dear all,
I am trying to perform an statistical analysis from FA Maps of two groups with 9 subjects each one using randomise function.
randomise is throwing an error at me after stalling at permutation 2. "Warning: tfce has detected a large number of integral steps. This operation may require a great deal of time to complete.
See attached more information.
Any suggestion about the issue?
Thanks in advance,
Alex
The call to the function is:
randomise -i <input> -o <output> -d <design.mat> -t <design.con> -n 5000 --T2 -V
The design matrix is:
/NumWaves 2
/NumPoints 18
/PPheights 1.000000e+00 1.000000e+00
/Matrix
1.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00
1.000000e+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 1.000000e+00
0.000000e+00 1.000000e+00
0.000000e+00 1.000000e+00
0.000000e+00 1.000000e+00
0.000000e+00 1.000000e+00
0.000000e+00 1.000000e+00
0.000000e+00 1.000000e+00
0.000000e+00 1.000000e+00
and contrast
/ContrastName1 group A > group B
/ContrastName2 group B > group A
/NumWaves 2
/NumContrasts 2
/PPheights 1.000000e+00 1.000000e+00
/RequiredEffect 2.801 2.801
/Matrix
1.000000e+00 -1.000000e+00
-1.000000e+00 1.000000e+00