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
>>
>
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