If you cannot save the design, then simply drop the last EV.
The contrast for linear change would then be, I think:
1.5 .5 -.5 -1.5
Individual comparisons would still be 1 -1, except for D versus E,
which would be 1.
See http://www.fmrib.ox.ac.uk/fsl/feat5/detail.html#ANOVA1factor4levelsRepeatedMeasures
Both models would produce the same statistical result.
Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General
Hospital and Harvard Medical School
Office: (773) 406-2464
=====================
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On Mon, Jan 24, 2011 at 10:04 PM, Gelareh Ahmadi
<[log in to unmask]> wrote:
> Dear Donald,
>
> I tried to designe the GLM that we discussed but it seems that there is a
> problem.
>
> Whenever I try to save it I will recieve this error:
>
> "Problem with processing model: Warning: at least one EV is (close to)
> linear combination to the others. You probably need to alter your design.
> (Design matrix is ranlk deficient-ratio of min:max eigenvaluesin SVD of
> matrix is 4.8605e-17)"
>
> I would appreciate if you could help me to solve this problem.
>
> Regards,
>
> Gelareh
>
>
>
> On Mon, Jan 24, 2011 at 10:06 AM, Gelareh Ahmadi
> <[log in to unmask]> wrote:
>>
>> Thank you very much for your help.
>>
>> Regards,
>>
>> Gelareh
>>
>> On Sun, Jan 23, 2011 at 1:26 AM, MCLAREN, Donald
>> <[log in to unmask]> wrote:
>>>
>>> Yes.
>>>
>>> On Saturday, January 22, 2011, Gelareh Ahmadi
>>> <[log in to unmask]> wrote:
>>> >
>>> > Dear Donald,
>>> >
>>> > Thank you for your reply.
>>> >
>>> > So if I understand correctly my design is correct, just in order to
>>> > show constant linear decrease I should add contrast as below:
>>> >
>>> > Group EV1 EV2 EV3 EV4 EV5
>>> > EV6 EV7
>>> > subj1 subj2 time1 time 2 time 3
>>> > time 4 time5
>>> > 1 1 0 1 0
>>> > 0 0 0
>>> > 1 0 1 1 0
>>> > 0 0 0
>>> > 1 1 0 0 1
>>> > 0
>>> > 0 0
>>> > 1 0 1 0 1
>>> > 0
>>> > 0 0
>>> > 1 1 0 0 0
>>> > 1 0 0
>>> > 1 0 1 0 0
>>> > 1 0 0
>>> > 1 1 0 0 0
>>> > 0 1 0
>>> > 1 0 1 0 0
>>> > 0 1 0
>>> > 1 1 0 0 0
>>> > 0 0 1
>>> > 1 0 1 0 0
>>> > 0 0 1
>>> >
>>> > Contrasts EV1 EV2 EV3 EV4 EV5
>>> > EV6 EV7
>>> > A-B 0 0 1 -1
>>> > 0 0 0 ( shows decrease FA between timepoint
>>> > 1&2)
>>> > B-C 0 0 0 1
>>> > -1 0 0
>>> > C-D 0 0 0 0
>>> > 1
>>> > -1 0
>>> > D-E 0 0 0 0
>>> > 0 1 -1
>>> > A-B-C-D-E 0 0 2 1
>>> > 0 -1 -2
>>> >
>>> > Is it right?
>>> >
>>> > Again thank you for your kind help.
>>> >
>>> > Regards,
>>> >
>>> > Gelareh
>>> >
>>> > On Sat, Jan 22, 2011 at 3:41 PM, MCLAREN, Donald
>>> > <[log in to unmask]> wrote:
>>> >
>>> > A constant linear decrease doesn't not mean A>B>C>D>E; rather on
>>> > average there is a constant decrease across time. If you want the
>>> > stated equation, then you need to form a conjunction.
>>> >
>>> > Typically, a constant linear decrease for 5 repetitions would be
>>> > defined as 2 1 0 -1 -2. The caveat is that this contrast could be
>>> > driven by A and E, but it would still be considered linear across
>>> > time.
>>> >
>>> > Hope this helps.
>>> >
>>> > Best Regards, Donald McLaren
>>> > =================
>>> > D.G. McLaren, Ph.D.
>>> > Postdoctoral Research Fellow, GRECC, Bedford VA
>>> > Research Fellow, Department of Neurology, Massachusetts General
>>> > Hospital and Harvard Medical School
>>> > Office: (773) 406-2464
>>> > =====================
>>> > This e-mail contains CONFIDENTIAL INFORMATION which may contain
>>> > PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED
>>> > and which is intended only for the use of the individual or entity
>>> > named above. If the reader of the e-mail is not the intended recipient
>>> > or the employee or agent responsible for delivering it to the intended
>>> > recipient, you are hereby notified that you are in possession of
>>> > confidential and privileged information. Any unauthorized use,
>>> > disclosure, copying or the taking of any action in reliance on the
>>> > contents of this information is strictly prohibited and may be
>>> > unlawful. If you have received this e-mail unintentionally, please
>>> > immediately notify the sender via telephone at (773) 406-2464 or
>>> > email.
>>> >
>>> >
>>> >
>>> > On Thu, Jan 20, 2011 at 11:55 PM, Gelareh Ahmadi
>>> > <[log in to unmask]> wrote:
>>> >> Dear FSL experts,
>>> >>
>>> >> My question is about designing GLM for repeated measure ANOVA.
>>> >>
>>> >> I have FA images from DTI scans for my subjcets. Each subject scanned
>>> >> in 5 different time points.
>>> >>
>>> >> I want to design a GLM which shows areas with decreased FA between
>>> >> time point 1&2, 2&3, 3 &4 , 4&5 and also areas which shows linear decrease
>>> >> from time point 1 to time point 5.
>>> >>
>>> >> I think for my first goal I should use ANOVA (1 factor-5 level),
>>> >> therefore for instance, for 2 subjects having scan in 5 time points, in
>>> >> order to show decrease FA between timepoint A&B, B&C, C&D and D&E, I should
>>> >> design:
>>> >>
>>> >> Group EV1 EV2 EV3 EV4 EV5
>>> >> EV6 EV7
>>> >> subj1 subj2 time1 time 2 time 3
>>> >> time 4 time5
>>> >> 1 1 0 1 0
>>> >> 0 0 0
>>> >> 1 0 1 1 0
>>> >> 0 0 0
>>> >> 1 1 0 0 1
>>> >> 0 0 0
>>> >> 1 0 1 0 1
>>> >> 0 0 0
>>> >> 1 1 0 0 0
>>> >> 1 0 0
>>> >> 1 0 1 0 0
>>> >> 1 0 0
>>> >> 1 1 0 0 0
>>> >> 0 1 0
>>> >> 1 0 1 0 0
>>> >> 0 1 0
>>> >> 1 1 0 0 0
>>> >> 0 0 1
>>> >> 1 0 1 0 0
>>> >> 0 0 1
>>> >>
>>> >> Contrasts EV1 EV2 EV3 EV4 EV5
>>> >> EV6 EV7
>>> >> A-B 0 0 1 -1
>>> >> 0 0 0 ( shows decrease FA between timepoint 1&2)
>>> >> B-C 0 0 0 1
>>> >> -1 0 0
>>> >> C-D 0 0 0 0
>>> >> 1 -1 0
>>> >> D-E 0 0 0 0
>>> >> 0 1 -1
>>> >>
>>> >> But I have no idea how I can show there is constant linear decrease
>>> >> from time point 1 to timepoint 5 ? I mean showing that FA1>FA2>FA3>FA4>FA5.
>>> >>
>>> >> I would highly appreciate if any one could let me know if Iam correct
>>> >> for the first goal and how I can solve my second problem.
>>> >>
>>> >> Best Regards,
>>> >>
>>> >> Gelareh
>>> >>
>>> > --
>>> > Gelareh Ahmadi, MD
>>> > PhD Candidate
>>> > Neuroimaging Group
>>> > Howard Florey Institute
>>> > University of Melbourne
>>> > VIC, Australia, 3010
>>> >
>>> > ph +61 3 8344 1904
>>> > fax +61 3 9347 0446
>>> >
>>>
>>> --
>>>
>>> Best Regards, Donald McLaren
>>> =================
>>> D.G. McLaren, Ph.D.
>>> Postdoctoral Research Fellow, GRECC, Bedford VA
>>> Research Fellow, Department of Neurology, Massachusetts General Hospital
>>> and
>>> Harvard Medical School
>>> Office: (773) 406-2464
>>> =====================
>>> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
>>> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
>>> intended only for the use of the individual or entity named above. If the
>>> reader of the e-mail is not the intended recipient or the employee or
>>> agent
>>> responsible for delivering it to the intended recipient, you are hereby
>>> notified that you are in possession of confidential and privileged
>>> information. Any unauthorized use, disclosure, copying or the taking of
>>> any
>>> action in reliance on the contents of this information is strictly
>>> prohibited and may be unlawful. If you have received this e-mail
>>> unintentionally, please immediately notify the sender via telephone at
>>> (773)
>>> 406-2464 or email.
>>
>>
>>
>> --
>> Gelareh Ahmadi, MD
>> PhD Candidate
>> Neuroimaging Group
>> Howard Florey Institute
>> University of Melbourne
>> VIC, Australia, 3010
>>
>> ph +61 3 8344 1904
>> fax +61 3 9347 0446
>
>
>
> --
> Gelareh Ahmadi, MD
> PhD Candidate
> Neuroimaging Group
> Howard Florey Institute
> University of Melbourne
> VIC, Australia, 3010
>
> ph +61 3 8344 1904
> fax +61 3 9347 0446
>
|