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Hi Matthieu,

It's difficult to tell as it depends on the degrees of freedom. However,
you can use the option "-zstat" so that the output statistics will be
converted to z. Then things should be in a more familiar range.

All the best,

Anderson


On 13 October 2015 at 10:47, Matthieu Vanhoutte <[log in to unmask]
> wrote:

> Dear Anderson,
>
> Thank you !
>
> If i used unthresholded t-statistic (or v-statistics) maps, what range
> have I to consider ? E.g., in one t-statistic map, T varies from -10 to 10
> so have I to consider negative, positive or both values according to my
> contrast ?
>
> Best regards,
>
> Matthieu
>
>
> 2015-10-11 10:17 GMT+02:00 Anderson M. Winkler <[log in to unmask]>:
>
>> Hi Matthieu,
>>
>> The -ise is needed still.
>>
>> All the best,
>>
>> Anderson
>>
>>
>> On 10 October 2015 at 21:09, Matthieu Vanhoutte <
>> [log in to unmask]> wrote:
>>
>>> Hi Anderson,
>>>
>>> So I will have to use the -eb and -vg options and not the -ise any more ?
>>> Isn't -ise option needed in m'y case ?
>>>
>>> Best regards,
>>>
>>> Matthieu
>>> Le 10 oct. 2015 12:26, "Anderson M. Winkler" <[log in to unmask]> a
>>> écrit :
>>>
>>>> Hi Matthieu,
>>>>
>>>> Hmm, I think may have meant to make a change but didn't. Well, it won't
>>>> matter in this case as the -ise is transparent to the block definitions
>>>> with within-block shuffling, so try repeating but using the options "-eb
>>>> VarianceGroup.csv -vg auto", that is, it will use the VG file as EB, and
>>>> from these, define automatically the actual VG. This is the same as "-eb
>>>> VarianceGroup.csv -vg VarianceGroup.csv".
>>>>
>>>> All the best,
>>>>
>>>> Anderson
>>>>
>>>>
>>>> On 10 October 2015 at 10:02, Matthieu Vanhoutte <
>>>> [log in to unmask]> wrote:
>>>>
>>>>> Dear Anderson,
>>>>>
>>>>> Many thanks for all these detailed explanations !
>>>>>
>>>>> However I used the -vg option un my command line with variance group
>>>>> differences between subjects in the .csv file, but still got t-stat and not
>>>>> v-stat outputed of PALM...
>>>>>
>>>>> How could it be possible ?
>>>>>
>>>>> Best regards,
>>>>>
>>>>> Matthieu
>>>>> Le 10 oct. 2015 10:42, "Anderson M. Winkler" <[log in to unmask]>
>>>>> a écrit :
>>>>>
>>>>>> There are two things going on:
>>>>>>
>>>>>> 1) The two contrasts can go in the same .csv file, i.e., one contrast
>>>>>> per row. This single file is supplied with -t. Or, as you did, the -d can
>>>>>> be supplied twice, although for this case doing this seems a bit cumbersome
>>>>>> (multiple designs can be considered, but usually when these are different).
>>>>>> It's fine though.
>>>>>>
>>>>>> 2) In the t-stat (produced when -vg is omitted, or if all subjects
>>>>>> are in the same VG), the results aren't necessarily valid, as the
>>>>>> assumptions of the test are violated twice: first the interpretation of
>>>>>> "there is a difference in means" only stands if the variances are the same,
>>>>>> and second, the unrestricted permutation test requires that the variances
>>>>>> are the same so as to preserve exchangeability. The v-stat (produced when
>>>>>> -vg is supplied) is valid.
>>>>>>
>>>>>> I'll reply the last one next.
>>>>>>
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> I have tried to launch PALM with one sample t-test on the 4D COPEs
>>>>>>> image (merges of all subjects' COPE), with the following command line :
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> *palm -i /SUBJECTDIR/4D_COPE.nii-d /SUBJECTDIR/design.csv-t
>>>>>>> /SUBJECTDIR/ContrastPos.csv-t /SUBJECTDIR/ContrastNeg.csv-vg
>>>>>>> /SUBJECTDIR/VarianceGroup.csv -ise-save1-p-o /SUBJECTDIR/Prefix*
>>>>>>>
>>>>>>> with design.csv a unique column vector of 1 (number of subjects =
>>>>>>> 7), ContrastPos.csv = 1 and ContrastNeg.csv = -1 (because I wanna test two
>>>>>>> t-contrast)  and
>>>>>>>
>>>>>>> VarianceGroupe.csv =[ 2 3 2 4 4 3 3
>>>>>>> ];
>>>>>>>
>>>>>>> and got this error message :
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> *Error using palm_takeargs (line 1217)More t-contrast files (2) than
>>>>>>> valid design files (1) were supplied.Error in palm_core (line 32)[opts,plm]
>>>>>>> = palm_takeargs(varargin{:});Error in palm (line
>>>>>>> 80)palm_core(varargin{:});Error in PALM_LEMP (line 3)*
>>>>>>>
>>>>>>> So in order to test sequentially contrast 1 then -1, I tried (is it
>>>>>>> not possible otherway ?) :
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> *palm -i /SUBJECTDIR/4D_COPE.nii-d /SUBJECTDIR/design.csv-t
>>>>>>> /SUBJECTDIR/ContrastPos.csv-d /SUBJECTDIR/design.csv-t
>>>>>>> /SUBJECTDIR/ContrastNeg.csv-vg /SUBJECTDIR/VarianceGroup.csv -ise-save1-p-o
>>>>>>> /SUBJECTDIR/Prefix*
>>>>>>>
>>>>>>> and got no significant results on corrected (fwep) t-stat and not
>>>>>>> *vstat* (as you mentioned above with the Aspin–Welch's*), *is it
>>>>>>> normal ?
>>>>>>>
>>>>>>> Is my design, contrasts and command line correct to test positive or
>>>>>>> negative longitudinal effect on my 7-subjects group ?
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>
>>
>