Dear Professor Smith:

Thank you for your reply.  As you suggested, I used the GLM GUI Wizard to
generate the design.con and design.mat files.  However, while running 
randomise
(after the TBSS processing stream) I get the same message with randomise
executing indefinitely without any further output.

"Warning: tfce has detected a large number of integral steps. This 
operation may
require a great deal of time to complete."

I've searched the forum and found possible solutions, but the ones that I've
come across do not seem to apply.  For example, the imaging data is free of
corruption on visual inspection and the order of the images matches the
design.con and design.mat files.  I've included the files, commands, 
and output
below.

Thank you again for your help in troubleshooting this problem.

Regards,

Roger

Order of subjects:

After_S1_FA     After_S2_FA     Before_S1_FA     Before_S2_FA

View design.mat:

/NumWaves     3
/NumPoints     4
/PPheights     2.000000e+00     1.000000e+00     1.000000e+00

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

View design.con:

/ContrastName1     "condition A > B"
/ContrastName2     "condition B > A"
/NumWaves     3
/NumContrasts     2
/PPheights     2.000000e+00     2.000000e+00
/RequiredEffect     3626504.500     3626504.500

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

The command and output are as follows:

[rogerjou@new-host stats]$ randomise -i all_FA_skeletonised.nii.gz -o
paired_tbss –m mean_FA_skeleton_mask.nii.gz -d design.mat –t design.con 
--T2 -V
--debug
randomise options: -i all_FA_skeletonised.nii.gz -o paired_tbss -m
mean_FA_skeleton_mask.nii.gz -d design.mat -t design.con --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 2.000000
4.000000 -1.000000 1.000000 2.000000

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

Input Contrast:
1.000000 0.000000 0.000000

Contrast rank: 1
Dof: 1 original dof: 1
Doing all 6 unique permutations
Starting permutation 1 (Unpermuted data)
statistic Maximum: 19213.1
Starting permutation 2
statistic Maximum: 1.69331e-10
Starting permutation 3
statistic Maximum: 2.64627e+16
Warning: tfce has detected a large number of integral steps. This 
operation may
require a great deal of time to complete.


Quoting Stephen Smith <[log in to unmask]>:

> Hi - you can use the model Wizard in the Glm GUi to setup a paired 
> t-test and save the design files.
>
> Cheers
>
>
>
> On 22 Feb 2012, at 18:31, Roger Jou wrote:
>
>> Dear FSL Experts,
>>
>> In case my question slipped through the cracks, I wanted to resend 
>> and reframe
>> the question.  In general, I wanted to know how to construct design.con and
>> design.mat files for paired t-test using TBSS and randomise (w/o using GUI).
>>
>> I've tried a different setup (included directly below this message), 
>> but keep
>> running into the same problem:
>>
>> "Warning: tfce has detected a large number of integral steps. This 
>> operation may
>> require a great deal of time to complete."
>>
>> Data looks good on inspection and randomise executing indefinitely 
>> but without
>> any further output.
>>
>> Thanks in advance for your help in this!
>>
>> Roger
>>
>> Order of subjects:
>> After_CE1264_FA
>> After_CE1710_FA
>> Before_CE1264_FA
>> Before_CE1710_FA
>>
>> View design.mat:
>> /NumWaves 4
>> /NumPoints 4
>> /PPheights 1 1 1 1
>> /Matrix
>> 1 0 1 0
>> 1 0 0 1
>> 0 1 1 0
>> 0 1 0 1
>>
>> View design.con:
>> /NumWaves 4
>> /NumContrasts 2
>> /PPheights 2 2
>> /Matrix
>> 1 -1 0 0
>> -1 1 0 0
>>
>>
>> Quoting Roger Jou <[log in to unmask]>:
>>
>>> My apologies...spelling error in design.con file.
>>>
>>> After correction, the program delivers this message after doing 2-3 
>>> permutions:
>>>
>>> Warning: tfce has detected a large number of integral steps. This 
>>> operation may
>>> require a great deal of time to complete.
>>>
>>> Yet, randomise is still executing but without any further output.
>>>
>>> Any help would be greatfully appreciated.
>>>
>>> Roger
>>>
>>> Quoting Roger Jou <[log in to unmask]>:
>>>
>>>> Dear FSL Community,
>>>>
>>>> I am trying to perform a paired t-test on FA of two subjects 
>>>> before and after an intervention using randomise.  The processing 
>>>> using FDT and TBSS has gone smoothly and the data quality looks 
>>>> good w/o signs of corruption.  However, I am stuck on how to 
>>>> create the proper design.con and design.mat files.  I have 
>>>> searched the FSL forum and inferring from item #032946 (which 
>>>> discusses four subjects, not two), I have set up the following:
>>>>
>>>> Order of subjects:
>>>> After_subj1
>>>> After_subj2
>>>> Before_subj1
>>>> Before_subj2
>>>>
>>>> View design.mat:
>>>> /NumWaves 3
>>>> /NumPoints 4
>>>> /PPheights 2 1 1
>>>> /Matrix
>>>> 1 1 0
>>>> 1 0 1
>>>> -1 1 0
>>>> -1 0 1
>>>>
>>>> View design.con:
>>>> /NumWaves 3
>>>> /NumConstrasts 2
>>>> /PPheights 2 2
>>>> /Matrix
>>>> 1 0 0
>>>> -1 0 0
>>>>
>>>> After typing:
>>>>
>>>> [rogerjou@localhost stats]$ randomise -i all_FA_skeletonised -o 
>>>> tbss -m mean_FA_skeleton_mask -d design.mat -t design.con --T2 -V 
>>>> --debug
>>>>
>>>> I get the following within a couple seconds:
>>>>
>>>> randomise options: -i all_FA_skeletonised -o tbss ?m 
>>>> mean_FA_skeleton_mask -d design.mat -t design.con --T2 -V --debug
>>>> Loading Data:
>>>> Data loaded
>>>> Finished, exiting.
>>>> [rogerjou@localhost stats]$
>>>>
>>>> Can someone please tell me what is going wrong here?
>>>> If the design.com and design.mat files are incorrect, can you 
>>>> please tell me the correct setup?
>>>>
>>>> Thanks in advance!
>>>>
>>>> Roger
>>>>
>>>
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director,  Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
> +44 (0) 1865 222726  (fax 222717)
> [log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
>
>
>