Hi,

As I understand it, "concentration" is about local intensity so that  
conserving
concentration when you are scaling an image (making the structure bigger
or smaller) will keep the intensity values within that region the same.
By comparison, conserving "total (amount)" tries to keep the product of
intensity and volume the same, so that if the volume increases then the
intensity within will decrease.

The behaviour of FLIRT is always to keep the intensity the same, thus
this would be "conserving concentration".  So you should be fine to use
either flirt, or scripts that call flirt, such as first_flirt.

Note that for FMRI analyses, it is common to do grand-mean intensity
normalisation which then rescales the intensities to have a fixed
overall mean across all dimensions (space and time).  If such a scaling
is done then it doesn't matter if you tried to correct for the original
flirt scaling or not, as it would be constant across space and time and
therefore would be factored out by this normalisation.  Only if you
are wanting to use the intensities in something like VBM would it make
a difference whether you tried to correct for the scaling (preserving
"total").

Hope this helps.
All the best,
	Mark



On 11 Oct 2007, at 03:35, Buyean Lee wrote:

> Hi Steve,
>
> Do you mean FSL normalization will not preserve the concentration?
>
> I am specifically paying attention to this issue due to the  
> following reason.
>
> I used to normalize the binding potential images of my PET images  
> using SPM2(5) in which it preserve concentration.
> Since I am not satisfied with the location of the subcortical  
> regions after normalization, I am looking for a method which can  
> improve the spatial normalization of the subcortical regions (if  
> you know one, let me know).
>
> I thought the spatial normalization used in FIRST (i.e.,  
> first_flirt) is promising.
> It seems to work better.  But, I don't know if 'first_flirt' will  
> preserver concentration or not.
>
> Thank you,
>
> Buyean
>
>
> -----Original Message-----
> From: Steve Smith <[log in to unmask]>
> To: [log in to unmask]
> Sent: Mon, 8 Oct 2007 11:04 pm
> Subject: Re: [FSL] FLIRT: Preserver what?
>
> Hi,
>
> FLIRT applies an affine-only transformation. If you wish to divide  
> the output image by the amount of volumetric scaling (to preserve  
> "concentration") you can extract the volumetric scaling factor  
> using avscale and then apply this easily with the -mul option  
> inside fslmaths.
>
> Cheers, Steve.
>
> On 8 Oct 2007, at 22:59, Buyean Lee wrote:
>
> > Dear FSL users,
> >
> > When one normalizes a image in SPM2(5), one can choose which >  
> parameter (e.g., concentration or total (=amount)) is going to be >  
> preserved.
> >
> > I read the FSL website and checked FLIRT options, but I can't  
> find > a similar option.
> >
> > Does FLIRT preserve the concentration?
> >
> > Thank you,
> >
> > Buyean
> > Check Out the new free AIM(R) Mail -- Unlimited storage and >  
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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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