Hi Anderson,
I will convert into z-score. But e.g. for a contrast of [-1], how could I
determine in z-stat which range of values (positive or negative) I should
use ?
Best regards,
Matthieu
2015-10-14 8:48 GMT+02:00 Anderson M. Winkler <[log in to unmask]>:
> 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 ?
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>
>>
>
