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Have a look at the doc (FLIRT and VECREG). It's pretty straightforward.
You can apply VECREG to the output of bedpostx as well (the dyads), unfortunately, you cannot easily apply that to the orientation samples (merged files). But you don't need to as you can always run probtrackx from any space/orientation that you like, and provide appropriate transformations to probtrackx (see doc).

Cheers
Saad

On 1 Jun 2012, at 15:57, Rodrigo Perea wrote:

> Thanks this is what I was looking for. Could you give me more details on how to rotate it? I tried it unsuccesfully. Also, I want to use this to apply it to the bedpostx folder but will make it more difficult, correct?
> 
> 
> 
> Hi - you could flirt your dti images to standard space and apply that transformation to V1 using vecreg.
> cingulum will be green though. add a 90deg rotation if you want is in blue..
> 
> Saad
> 
> On 1 Jun 2012, at 15:35, Rodrigo Perea wrote:
> 
>> Thanks for your response but imagine that I want to see superior-inferior  blue color of the cingulum but if the cingulum is diagonal to the superior-inferior axis, then the color will be between green and blue. Is there any way I can make the cingulum straight blue? I hope this make sense...
>> 
> 
> --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
> 
> JR Hospital, Headington, OX3 9DU, UK
> (+44)1865-222466  (fax 717)
> www.fmrib.ox.ac.uk/~saad
> 
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> 
> 

--
Saad Jbabdi
University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466  (fax 717)
www.fmrib.ox.ac.uk/~saad