Hi Anderson,
As one timepoint is knocked out from each subject in design 2 and 3, if I enter in model only the data of timepoint 1 or 2, the design 2/3 and this one should give the same results?
EB EV1 EV2
1 1 0
1 1 0
1 1 0
1 1 0
1 1 0
1 0 1
1 0 1
1 0 1
Thanks a lots,
Best regard,
Kim TD
On Wed, 20 Jan 2016 08:58:10 +0000, Anderson M. Winkler <[log in to unmask]> wrote:
>Hi Kim,
>
>Design 1 tests within-subject effects (if there is a difference between
>timepoints, for instance, and interactions). Design 4 tests between-subject
>effects (if there is a group difference across both timepoints).
>
>In design 1, the subject-specific intercepts are entered as additional,
>confound EVs. In design 4, the subject-specific slopes are entered as
>additional, confound EVs.
>
>Designs 2 and 3 do something else: for these designs either of the two
>timepoints is knocked out from each subject, such that it's as if these
>marked timepoints didn't exist. Design 2 causes t2 to be ignored, such that
>comparisons are between groups on what concerns timepoint 1 only. Design 3
>causes t1 to be ignored, such that comparisons are between groups on what
>concerns timepoint 2 only.
>
>So, please note that for designs 2 and 3, it's the opposite than what you
>wrote below, i.e., design 2 tests timepoint 1, whereas design 3 tests
>timepoint 2.
>
>All the best,
>
>Anderson
>
>
>On 19 January 2016 at 13:07, Kim TRAN <[log in to unmask]> wrote:
>
>> Hi Anderson,
>>
>> I have a small question, what is the difference between design1 et design4
>> in the file that you showed me? I think they're kind of similar. Design2 is
>> used for testing 2nd scan because values for EV3-Ev22 are in the 2nd scan,
>> and design3 is used for the 1st scan, isn't it? Could you check this for
>> me? Thank you very much,
>>
>> Best regard,
>>
>> Kim
>>
>> On Sat, 14 Nov 2015 07:44:22 +0000, Anderson M. Winkler <
>> [log in to unmask]> wrote:
>>
>> >Hi Kim,
>> >
>> >These tests need to go in separate designs. You can still correct across
>> >all with -corrcon in PALM. Or prune your hypotheses to what is more
>> >relevant (presumably the effect of the treatment, which is in design 1),
>> >and run that in randomise or FEAT.
>> >
>> >All the best,
>> >
>> >Anderson
>> >
>> >On 13 November 2015 at 09:20, Kim TRAN <[log in to unmask]> wrote:
>> >
>> >> Hi Anderson,
>> >>
>> >> I am so sorry for having bothered you. I've found the response in others
>> >> sheets of your file. It's all that I want, but I cannot make it just
>> with
>> >> one design?
>> >>
>> >> Thanks a lots,
>> >> Kim
>> >>
>> >> On Fri, 13 Nov 2015 08:58:05 +0000, Kim TRAN <[log in to unmask]>
>> >> wrote:
>> >>
>> >> >Hi Anderson,
>> >> >
>> >> >Thank you very much for your reply. The contrasts C1 and C2 in your
>> >> attached file are the differences (t1-t2) for each group? Because I
>> want to
>> >> run a one side t-test, could I add these 2 more contrasts for a complete
>> >> approach:
>> >> >C5: -1 0 0 0 0 ... (t2-t1 in group 1)
>> >> >C6: 0 -1 0 0 0 ... (t2-t1 in group 2)
>> >> >
>> >> >Might they change the interpretation of C3 and C4?
>> >> >
>> >> >Thanks a lots,
>> >> >
>> >> >Kim
>> >> >
>> >> >
>> >> >On Fri, 13 Nov 2015 07:46:47 +0000, Anderson M. Winkler <
>> >> [log in to unmask]> wrote:
>> >> >
>> >> >>Hi Kim,
>> >> >>
>> >> >>Design is fine, but the contrasts need to be changed. Please, delete
>> all
>> >> of
>> >> >>them and instead use:
>> >> >>
>> >> >>C1: 1 -1 0 0 0 0 ....
>> >> >>C2: -1 1 0 0 0 0 ....
>> >> >>
>> >> >>These will test the effect of the treatment, and can be used in FEAT,
>> >> >>randomise, or PALM.
>> >> >>
>> >> >>However, it seems you also want to compare groups in the 1st and 2nd
>> >> scans,
>> >> >>is this correct? If yes, please see at this link
>> >> >><
>> >>
>> https://dl.dropboxusercontent.com/u/2785709/outbox/mailinglist/design_kimtran.ods
>> >> >
>> >> >>the relevant designs. You'd need to use PALM, in which case you can
>> also
>> >> >>correct across all of them in the same run (option -corrcon). Include
>> the
>> >> >>options -whole and -within (both) if you take this route.
>> >> >>
>> >> >>All the best,
>> >> >>
>> >> >>Anderson
>> >> >>
>> >> >>
>> >> >>
>> >> >>On 12 November 2015 at 16:24, Kim TRAN <[log in to unmask]> wrote:
>> >> >>
>> >> >>> Dear FSL experts,
>> >> >>>
>> >> >>> I have 8 subjects, each scanned 2 times at 2 times point. The fisrt
>> 5
>> >> >>> subjects are in drug group, and another 3 are in placebo group. I
>> want
>> >> to
>> >> >>> compare results of those 2 groups. Are the design and contrasts
>> below
>> >> >>> correct?
>> >> >>>
>> >> >>> EB EV1 EV2 EV3 EV4 EV5 EV6 EV7 EV8
>> >> >>> EV9 EV10
>> >> >>> 1 1 0 1 0 0 0 0 0
>> >> 0
>> >> >>> 0
>> >> >>> 1 -1 0 1 0 0 0 0 0
>> >> 0
>> >> >>> 0
>> >> >>> 2 1 0 0 1 0 0 0 0
>> >> 0
>> >> >>> 0
>> >> >>> 2 -1 0 0 1 0 0 0 0
>> >> 0
>> >> >>> 0
>> >> >>> 3 1 0 0 0 1 0 0 0
>> >> 0
>> >> >>> 0
>> >> >>> 3 -1 0 0 0 1 0 0 0
>> >> 0
>> >> >>> 0
>> >> >>> 4 1 0 0 0 0 1 0 0
>> >> 0
>> >> >>> 0
>> >> >>> 4 -1 0 0 0 0 1 0 0
>> >> 0
>> >> >>> 0
>> >> >>> 5 1 0 0 0 0 0 1 0
>> >> 0
>> >> >>> 0
>> >> >>> 5 -1 0 0 0 0 0 1 0
>> >> 0
>> >> >>> 0
>> >> >>> 6 0 1 0 0 0 0 0 1
>> >> 0
>> >> >>> 0
>> >> >>> 6 0 -1 0 0 0 0 0 1
>> >> 0
>> >> >>> 0
>> >> >>> 7 0 1 0 0 0 0 0 0
>> >> 1
>> >> >>> 0
>> >> >>> 7 0 -1 0 0 0 0 0 0
>> >> 1
>> >> >>> 0
>> >> >>> 8 0 1 0 0 0 0 0 0
>> >> 0
>> >> >>> 1
>> >> >>> 8 0 -1 0 0 0 0 0 0
>> >> 0
>> >> >>> 1
>> >> >>>
>> >> >>> Contrast:
>> >> >>> mean G1, 1st scan 5 0 1 1 1 1
>> >> 1
>> >> >>> 0 0 0
>> >> >>> mean G1, 2nd scan -5 0 1 1 1 1
>> >> 1
>> >> >>> 0 0 0
>> >> >>> mean G2, 1st scan 0 3 0 0 0 0
>> >> 0
>> >> >>> 1 1 1
>> >> >>> mean G2, 2nd scan 0 -3 0 0 0 0
>> >> 0
>> >> >>> 1 1 1
>> >> >>> G1 > G2, 1st scan 5 -3 1 1 1 1
>> >> 1
>> >> >>> -1 -1 -1
>> >> >>> G1 > G2, 2nd scan -5 3 1 1 1 1
>> >> 1
>> >> >>> -1 -1 -1
>> >> >>>
>> >> >>> Any help you can provide will be greatly appreciated.
>> >> >>> Best regard,
>> >> >>> Kim
>> >> >>>
>> >> >>
>> >>
>> >
>>
>