Dear Sven,
2.3 is the value that will be used as the cluster-forming
threshold for your f-stat(s), if you don't want
cluster-corrected results then you can use the --T2
option or even just -x for voxelwise results. The F-test
is a statistic type, --T2, -F, -x etc are just various
methods for dealing with multiple-comparisons.
I hope this helps,
Kind Regards
Matthew
> Dear Matthew,
>
> this seems to have worked but you managed to confuse me a little more with
> regards to the F-test. Sorry. :-) You say ("e.g. -F 2.3"). I thought that
> if I only specified one F-test in my design and checked the three boxes,
> this would be a combined F-test. If what you are writing is correct in my
> case, then should I write -F 1.2.3 in order to get the full F? Sorry, I
> don't understand the "2.3"....
>
> Another quick question:
>
> Can I combine the F-test with the --T2 option or are these exclusive? I am
> not sure I quite understand whether these two options can be run together
> in one analysis or whether they should be run separately.
>
> Thanks so much for your help,
>
> sven
>
>
> ___________
>
>
>
>
> Hello Sven,
> It looks like you are using a lower case ( -f ) for the
> F-test cluster threshold option, this should be a
> capital F ( e.g. -F 2.3 ) - can you try this and let us
> know if the error changes?
>
> Kind Regards
>
> Matthew
>
>> Dear FSLers,
>>
>> I am new to FSL and am currently analysing 4 groups DTI TBSS data and
>> have
>> worked my way through the tutorial and posts on the mailing list.
>> However,
>> I am still confused with the F-Test.
>>
>> If I include the -f design.fts option but not specify an -F [number]
>> option, I get an error message that no specific option was selected but
>> if
>> I do say -F 1 then I get another error message. So concretely, I had
>> used
>> the example on the TBSS stats webpage:
>>
>> randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d
>> model_test1.mat -t model_test1.con -f model_test1.fts -n 5000 -c 2 -V
>>
>> Message:
>> Loading Data:
>> Data loaded
>> 1.16979e+44 permutations required for exhaustive test of f-test 1
>> Doing 5000 random permutations
>> Warning! No output options selected. Outputing raw tstat only
>>
>> I had then tried
>>
>> randomise options: -i all_FA_skeletonised -o tbss -m
>> mean_FA_skeleton_mask
>> -d model_test1.mat -t model_test1.con -f model_test1.fts -n 5000 -c 2 -f
>> 1
>> -V
>>
>> but got
>> Loading Data: ERROR: Program failed
>>
>> An exception has been thrown
>> Unable to open 1
>>
>> Exiting
>>
>> _______
>>
>> If my design matrix is such that
>> F-TEST
>> 1 -1 0 0 check
>> 1 0 -1 0 check
>> 1 0 0 -1 check
>> ……
>> …… set of remaining t-contrasts here without selection of F, e.g.,
>> 0 0 1 -1 not checked
>> … etc
>>
>> What option should I use in randomize to get the output for my F-test?
>> Should I use a combination of these to specify the contrast or can I
>> ignore the error and check this once the statistics have run?
>>
>>
>> Many thanks in advance for any suggestions!
>>
>> Sven
>>
>
>
