Hi,
On 15 May 2007, at 17:30, Cinly Ooi wrote:
> 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
You probably don't need this for your purposes - this is the design
efficiency calculation - you can just set those to 1 or something.
> for design.con.
>
>
> I figure design.grp is the data for the column named Group in GLM's
> GUI
indeed
> and that design.fsf is the description of setup of the GUI and
> something more.
yes - it's the TCL code needed to save the complete FEAT GUI settings
> 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.
I'm not sure what you mean by "orthogonalized contrast" ?
Cheers.
>
> 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
------------------------------------------------------------------------
---
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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