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FSL  May 2007

FSL May 2007

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Subject:

Re: design.con and design.mat in TBSS step 5

From:

Cinly Ooi <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Tue, 15 May 2007 17:30:43 +0100

Content-Type:

text/plain

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Parts/Attachments

text/plain (105 lines)

Dear Prof Smith,

 Thanks for the quick reply.

 I did read the design.mat and design.con file, but also explored
design.grp and design.fsf

 By experimenting with values, I managed to guess that for design.mat :

 /NumWaves == number of EVs
 /NumPoints == number of rows
 /PPheights = an array of the range of number for EV, i.e. [max(EV(n)-min(EV(n)]

 For design.con,
 /ContrastName{n} == name of contrast{n}
  /NumContrasts == number of contrast


 But cannot figure out how to generate

 /RequiredEffects

 for design.con.


 I figure design.grp is the data for the column named Group in GLM's
GUI and that  design.fsf is the description of setup of the GUI and
something more.

 I have yet to figure out how to generate the orthogonalized contrast.
Any tips. All I need is pointers to the program file generating them
and I should be able to figure it out from there.

 Thank you in advance and Best regards,
 Cinly



> On 15/05/07, Steve Smith <[log in to unmask]> wrote:
> > HI - if you've got as far as the raw ascii matrices then writing a
> > script to add the header is very easy - just look at existing files
> > to see the format.
> > Cheers.
> >
> >
> > On 15 May 2007, at 13:44, Cinly Ooi wrote:
> >
> > > Dear All,
> > >
> > > In TBSS step 5 (http://www.fmrib.ox.ac.uk/fsl/tbss/index.html ) ,
> > > when calling
> > >
> > > randomise -d design.mat -t design.con
> > >
> > > We normally use GLM Setup->Higher Level/Non time series design.
> > >
> > > We are now trying to integrate the process in our processing
> > > pipeline where we have "partial" design.mat and design.con already,
> > > i.e., we have the EVs for design.mat and contrasts for design.con
> > >
> > > In other words, we have
> > > design_raw.mat=
> > > 1 0
> > > 1 0
> > > 1 1
> > > 1 1
> > > 0 1
> > > 0 1
> > >
> > > and design_raw.con=
> > > -1  1
> > > 1  -1
> > >
> > > and we will like to transform it into the standard design.mat and
> >  > design.con. Is there any program that can read in our design_raw.*
> > > and perform the conversion?
> > >
> > >
> > > Thank you in advance and Best Regards,
> > > Cinly
> >
> >
> > ------------------------------------------------------------------------
> > ---
> > 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
> > ------------------------------------------------------------------------
> > ---
> >
>
>
>
> --
> Best Regards,
> Cinly



-- 
Best Regards,
Cinly

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