Hi Steve and Alison,
I had this problem when setting up big designs (either lots of EVs or lots
of inputs, usually both), in that only some of the drop-down menus and boxes
were drawn in the GUI window (the drawing of boxes started from bottom
right, but never made it all the way to top left). I think clearing disk
space and degfragmenting C: may have helped a bit, but in the end I had to
edit the design.fsf file manually to set it up.
perhaps a problem with feat in windows? I had the same problem on laptop and
on desktop and with older and latest versions of FEAT.
cheers,
nick
----- Original Message -----
From: "Steve Smith" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Wednesday, May 02, 2007 9:58 AM
Subject: Re: [FSL] design matrix
Hi - I'm not quite sure what you're saying is happening. I don't
think there's any limit to the number of EVs in the current version
of FEAT - when I try to set 44 EVs it works fine, and includes a
scrollbar at the bottom to let you scroll across to the higher-
numbered EVs. Is your screen large enough to see all this? I'm not
sure what you mean by "grey section"?
Cheers.
On 30 Apr 2007, at 14:29, Alison Watson wrote:
> Many thanks for your help. I tried to set up the design matrix as
> suggested (see
> below) with 11 subjects x 4 scans I have 44 evs. When I try to enter 44
> evs I
> get an error in the design matrix (GLM)window; I get a grey section in
> the
> window for the the first 19 inputs. It appears that I can only enter a
> maximum
> of 35 evs. Has anyone had this problem before?
>
> Many thanks.
>
> Alison
>
>
>
> Quoting Mark Woolrich <[log in to unmask]>:
>
>> Hi Alison,
>>
>> I would do this in 3 levels. Do a fixed effect analysis at the second
>> level, which estimates separate contrasts for all of the individual
>> subject before and after differences, e.g.:
>>
>> subj1 before treat -1 1 0 0 0 0 0 0 ...
>> after treat 1 1 0 0 0 0 0 0 ...
>> before cont 0 0 -1 1 0 0 0 0 ...
>> after cont 0 0 1 1 0 0 0 0 ...
>> subj2 before treat 0 0 0 0 -1 1 0 0 ...
>> after treat 0 0 0 0 1 1 0 0 ...
>> before cont 0 0 0 0 0 0 -1 1 ...
>> after cont 0 0 0 0 0 0 1 1 ...
>> etc...
>>
>> contrast1(sub1,treat) 1 0 0 0 0 0 0 0
>> contrast2(sub1,cont) 0 0 1 0 0 0 0 0
>> contrast3(sub2,treat) 0 0 0 0 1 0 0 0
>> contrast4(sub2,cont) 0 0 0 0 0 0 1 0
>>
>> etc...
>>
>> Note that you need EVs that model the individual (treatment or
>> control) subject means.
>>
>> The at a third level do a mixed effect analysis for a control-
>> treatment paired difference (see http://www.fmrib.ox.ac.uk/fsl/feat5/
>> detail.html#PairedTwoGroupDifference for inspiration) between
>> appropriate subjects' contrasts from the second level:
>>
>> contrast1(sub1,treat) 1 1 0 ...
>> contrast2(sub1,cont) -1 1 0 ...
>> contrast3(sub2,treat) 1 0 1 ...
>> contrast4(sub2,cont) -1 0 1 ...
>> etc...
>>
>> contrast 1 0 0 ...
>>
>> Best regards, Mark.
>>
>> ----
>> Dr Mark Woolrich
>> EPSRC Advanced Research Fellow University Research Lecturer
>>
>> Oxford University Centre for Functional MRI of the Brain (FMRIB),
>> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
>>
>> Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~woolrich
>>
>>
>>
>>
>> On 25 Apr 2007, at 14:51, Alison Watson wrote:
>>
>>> I have 11 subjects each had 2 scanning sessions a treatment session
>>> and a control session. During each session subjects has 2 separate
>>> scans one pre drug and one post drug. I want to do the following
>>> contrast
>>>
>>>
>>>
>>> [treatment (post - pre) – control(post-pre)] to image treatment
>>> increases related to control and [control (post - pre) – treatment
>>> (post-pre)] to image treatment decreases relative to control. I am
>>> not sure how to set up the design matrix. Can anyone help please?
>>>
>>>
>>>
>>> Many thanks
>>>
>>>
>>>
>>> Alison
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>
>
>
> --
> Alison Watson
> Human Pain Research Group
> Clinical Sciences Building
> Hope Hospital
> Salford
> UK
> M6 8HD
> Tel 0161 206 4529
> www.hop.man.ac.uk/painresearch
------------------------------------------------------------------------
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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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