Hi, Anderson and all,
As Anderson said, the "Group" in the FEAT GUI does not stand for the
real "experimental
group" as used in the common statistical book. I have thought it over. It
seems to me that in fact, the FSL does not have a method to differ the
paired t-test (i.e., same group, repeated measurement) and independent
t-test (i.e,, different groups, same measurement).
Am I correct?
Thank you very much,
Sim Luck
On Tue, Feb 21, 2017 at 1:49 PM, Sim Luck <[log in to unmask]> wrote:
> Hi, Anderson,
>
> Thanks so much for so insightful comments.
>
> I now get to know the real definition "group" in FSL. This opens a new
> question: how to differ the real "experimental group" in the FSL, then?
> Is there any a good method for this?
>
> Thank you very much,
> Sim Luck
>
>
>
> On Tue, Feb 21, 2017 at 4:26 AM, Anderson M. Winkler <
> [log in to unmask]> wrote:
>
>> Hi Sim Luck,
>>
>> On 20 February 2017 at 22:59, Sim Luck <[log in to unmask]> wrote:
>>
>>> Hi, FSL experts,
>>>
>>> I am a beginner with FSL. Previously I asked one question on the
>>> independent t-test with FSL (e.g., patients, healthy controls). Two experts
>>> suggested me simply using the "1" as "Group" for both patients and healthy
>>> controls. I agree as if I used "1" for one group and "2" as the other
>>> group, I did not observe any effects between the groups. I was thinking
>>> that this FSL approach is different from the common behavioral data
>>> analysis.
>>>
>>
>> The information from the "Group" setting is stored in a file named
>> something as "design.grp", and this file takes different roles depending
>> whether the analysis is used in FEAT, in PALM, or in randomise. In all
>> three cases, the "Group" does not refer to "experimental group". Instead,
>> it refers to "variance group" (VG) in FEAT, to "exchangeability block" (EB)
>> in randomise, and to either VG or EB in PALM, depending on whether it's
>> supplied with the options "-vg" or "-eb".
>>
>> In FEAT, unless there is reason to suspect (or assume) that the variances
>> for the groups are different, all subjects should belong to group "1". If
>> variance groups are defined, then the design must be "separable", that is,
>> the design must be such that, if the observations are sorted by group, the
>> design can be constructed by direct sum (i.e., block-diagonal
>> concatenation) of the design matrices for each group separately.
>>
>> In randomise, the same "Group" setting can be supplied with the option
>> "-e design.grp", defining exchangeability blocks. Observations within a
>> block can only be permuted with other observations within that same block.
>> If the option --permuteBlocks is also supplied, then the EBs must be of the
>> same size, and the blocks as a whole are permuted.
>>
>> In PALM, using "-eb design.grp" has the same effect as "-e design.grp" in
>> randomise. Further using "-whole" is equivalent to using "--permuteBlocks"
>> in randomise. However, it's also possible to use "-whole -within", meaning
>> that the blocks as a whole are shuffled, and further, observations within
>> block can be shuffled. In PALM the file supplied with the option "-eb" can
>> have multiple columns, indicating multi-level exchangeability blocks, which
>> are useful in designs with more complex dependence between observations.
>> Using "-vg design.grp" causes PALM to use the v- or G-statistic, which are
>> replacements for the t- and F-statistics respectively for the cases of
>> heterogeneous variances.
>>
>> In both FEAT and PALM, using "group" as VG will only make difference if
>> such variance groups aren't balanced.
>>
>>
>>>
>>> Now I want to do the paired t-test (the same patients were tested two
>>> times, before the treatment, and after the treatment). My quick thought is
>>> that of course, I should use the "1" as group for both sessions ("before"
>>> session and "after" sessions). But my problem is that I did not find any
>>> effect of treatment - this does not make sense to me. So I want to confirm
>>> with the FSL experts to see if I am wrong on anything.
>>>
>>
>> For the paired t-test in FEAT, you can leave the "Group" column as all
>> ones. The same test in PALM or in randomise requires one exchangeability
>> block per subject, so you'd use the "Group" column to define the EBs, and
>> supply them with "-e design.grp" (randomise) or "-eb design.grp" (PALM).
>>
>> Hope this clarifies the matter!
>>
>> All the best,
>>
>> Anderson
>>
>>
>>
>>> Here I attach some details in 2 slides - see the attachment. Could any
>>> experts advise me, if I am incorrect on anything?
>>>
>>> Thank you very much,
>>> Simi Luck
>>>
>>
>>
>
