You need to use a 3 column format to specify the exact onset
and duration of each stimulus. The square wave setup is
not suitable for this type of design. The 3 column format is
described in the online documentation.
All the best,
Mark
On 3 May 2010, at 09:49, Reem Jan wrote:
> Hi Steve
>
> Thank you for your reply. I'm actually about to attend the FSL
> course end of May but I wanted to try analyzing a couple of subjects
> fMRI data prior to coming. You have helped me with my previous
> question, however Im still undecided about how to set up my model. I
> do have 3 EVs (A, B, C) but they are also repeated within the same
> session ie A B C C B A. How can I let FEAT know that?
> Also, all my conditions have identical durations so how do I make
> them different? Unless I'm supposed to alter the 'phase' to reflect
> that?
>
> Many thanks for your help.
>
> Cheers
> Reem
>
>
> On 3/05/2010, at 19:06, "Stephen Smith" <[log in to unmask]> wrote:
>
>> Hi - from the sounds of it you setup all 3 EVs to be identical.
>> This is why you get this error message.
>> Cheers.
>>
>>
>> On 3 May 2010, at 07:35, Reem Jan wrote:
>>
>>> Hello FSL users
>>>
>>> Can someone please help me with this error message:
>>> Problem with processing the model: Warning: at least one EV is
>>> (close
>>> to) a linear combination of the others. You probably need to alter
>>> your
>>> design. (Design matrix is rank deficient - ratio of min:max
>>> eigenvalues
>>> is SVD of matrix is 8.88555e-34)
>>>
>>> I got this error message when I tried to View Design after setting
>>> up my
>>> model of 3 EVs, for each EV I entered the following values:
>>> Off = 16, On = 40, Phase = 16. I chose a square basic shape and left
>>> convolution as it is in the default settings (Gamma). Where did I go
>>> wrong?
>>>
>>> Many thanks in advance for your help.
>>>
>>> Kind regards
>>> Reem
>>>
>>> On Wed, 2010-03-31 at 19:11 +0100, Stephen Smith wrote:
>>>> Hi
>>>>
>>>> On 29 Mar 2010, at 02:18, Reem Jan wrote:
>>>>
>>>>> Dear FSL experts
>>>>>
>>>>> I am a brand new FSL user. I run a blocked Stroop task with fMRI,
>>>>> and I
>>>>> have previously analysed some of my data using SPM. I am trying to
>>>>> learn
>>>>> using FEAT and unfortunately I'm getting stuck at very preliminary
>>>>> stages.. Can someone please help?
>>>>> I'll explain my paradigm and what I have been entering in the
>>>>> GUI so
>>>>> far..
>>>>>
>>>>> My TR is 3 seconds
>>>>> I have 118 functional images per subject.
>>>>> The blocked Stroop task I use is set up as follows:
>>>>> Rest (16sec) - Neutral condition (40sec) - Rest (16sec) -
>>>>> Congruent
>>>>> condition (40sec) - Rest (16sec) - Incongruent condition (40sec) -
>>>>> Rest
>>>>> (16sec) - Incongruent condition (40sec) - Congruent condition
>>>>> (40sec) -
>>>>> Rest (16sec) - Neutral condition (40sec)
>>>>>
>>>>> I have several questions:
>>>>> 1) Does that make my design rA-rB-rC-rC-rB-rA?
>>>>>
>>>>
>>>>
>>>> Yes; you won't explicitly model the rest conditions - you will have
>>>> EV1=A EV2=B EV3=C
>>>>
>>>>>
>>>>> 2) Is my 'high pass filter cutoff' = r+A+r+B+r+C
>>>>> (16+40+16+40+16+40)
>>>>> =
>>>>> 168sec?
>>>>>
>>>>
>>>>
>>>> It depends on your contrasts - have a read of the Smith NeuroImage
>>>> paper on efficiency, and a play with the efficiency estimator in
>>>> FEAT.
>>>>
>>>>> 3) My data is acquired with interleaved order but for a blocked
>>>>> design
>>>>> like mine, do I need to use slice time correction? (I know I don't
>>>>> tick
>>>>> that option in SPM).
>>>>>
>>>>
>>>>
>>>> No, we generally recommend against that.
>>>>
>>>>> 4) I struggled with setting up a full model despite reading the
>>>>> instructions on FSL webpage. According to the information I
>>>>> supplied
>>>>> above, do I have 3 or 6 EVs? as I have a repetition of each
>>>>> condition as
>>>>> described above.
>>>>>
>>>>
>>>>
>>>> You have 3 "original" EVs, which by default will get turned into 6
>>>> "real" EVs once the temporal derivatives are added by FEAT for you.
>>>>
>>>>
>>>> Cheers.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>
>>>>> I greatly appreciate your time and advice.
>>>>>
>>>>> Kind regards
>>>>> Reem
>>>>>
>>>>>
>>>>
>>>>
>>>> ---------------------------------------------------------------------------
>>>> Stephen M. Smith, Professor of Biomedical Engineering
>>>> Associate Director, Oxford University FMRIB Centre
>>>>
>>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>>> +44 (0) 1865 222726 (fax 222717)
>>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>>> ---------------------------------------------------------------------------
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>> ---------------------------------------------------------------------------
>>
>>
>>
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