In the case of a single covariate (ie a single EV) you should make sure that the EV values are demeaned (across all subjects) before putting into the GLM GUI or by hand into the design.mat file. Once you've setup the GLM GUI you can save the design.mat and design.con to file - if this is still confusing you can see the worked practical examples in the FSL course material online.    

As you are not modelling the mean of the data in this case you should use the -D option to also demean the data when you run randomise.

Steve.


On 9 Dec 2009, at 11:21, Mark Walterfang wrote:

Hi Stephen & group

I have the same question, and posed it some time ago to the group without receiving a response. For a single group with a single variable of interest (e.g. Cognitive or symptom score), in the GLM GUI, we would select non-timeseries design, # of inputs is the n of the group, number of main EVs would equal 1, zero additional EVs, and then the variable is input into the EV1 column (with all in the Group column remaining as 1)? Is this correct? On the randomise manual page, which I think I’ve gone over dozens of times regarding this, I’ve never quite been able to work out the syntax for an analysis like this, so some guidance as to the syntax would be welcomed. (On the web page, http://www.fmrib.ox.ac.uk/fsl/randomise/index.html#examples , I assume the 1-sample t-test example isn’t what we are looking for as it says it does not require design.con or design.mat.)

Rgds

Mark Walterfang


On 9/12/09 10:12 PM, "Stephen Smith" <[log in to unmask]> wrote:

Hi  please see the TBSS and randomise manual pages.   You do not use the FEAT GUI with TBSS-preprocessed data, you create a design matrix either by hand or with the "Glm" GUI, and then run randomise.

Cheers.



On 9 Dec 2009, at 04:48, Chihiro Hosoda wrote:

Hi,

I would like to perform a single group tbss correlation  of a behavioral test
scores with FA maps  

The question I have relates to setting  up the design matrix using the
GLM GUI.(FEAT)

Are  the following steps correct?

1. first-level analysis:
    Are the number of input images the number of subjects?
    Select the personal FA data on "select the 4D data" ?

2. High-level analysis:
   Chose the feat directory which I made in above first level analysis
on "select the 4D data" ?

I tried above steps, but I cannot make the stats folder and cope images in
first level analysis (within feat folder) so when I tried to high -level analysis
the warning was appeared, Why?

Besides, when I tried to high -level analysis, the following error was appeared
[Registration has not been run for all of the FEAT directories that you have
select for group analysis]

Would you do me the favor of telling me the correct way to generate
design.mat for TBSS correlation analysis.

Chihiro


 

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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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