Hi Jake,
The -o option just specifies the root in the output file names. As the
warning message indicates, you need to specify an actual output
statistic of some sort that you want to do permutations on -- see the -
T, -c, and -C options for some possibilities. Also, you might want to
specify a mask image of some sort.
cheers,
-MH
On Mon, 2012-04-23 at 18:58 +0100, Jake wrote:
> Dear FSLers,
>
> I am attempting to run a contrast in randomise and it appears that only one permutation completes although it states 3432 permutations would be exhaustive. If I do -n 5000, -n 0, or do not specify n, randomise still only performs one permutation. If someone could help me to understand where my mistake may be I would greatly appreciate it!
>
> Best,
> Jake
>
> Here's the output:
>
> randomise -i ASL_7pat_7ctrl_4D_smth.nii.gz -o 7pv7c_n5000_sm5 -n 5000 -d design.mat -t design.con
> randomise options: -i ASL_7pat_7ctrl_4D_smth.nii.gz -o 7pv7c_n5000_sm5 -n 5000 -d design.mat -t design.con
> Loading Data:
> Data loaded
> 3432 permutations required for exhaustive test of t-test 1
> Doing all 3432 unique permutations
> Warning! No output options selected. Outputing raw tstat only
> Starting permutation 1 (Unpermuted data)
> 3432 permutations required for exhaustive test of t-test 2
> Doing all 3432 unique permutations
> Warning! No output options selected. Outputing raw tstat only
> Starting permutation 1 (Unpermuted data)
> Finished, exiting.
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