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Yep, Andreas is right, and this voxelwise version of SIENA will be (in
beta form) in the new release of FSL in (hopefully) a week or two.

Cheers.



On Fri, 27 Aug 2004, Andreas Bartsch wrote:

> Hi,
>
> there is a regional extension to SIENA (siena_flow2tal script in the current release; see 1) De Stefano N et al.: Voxel-level cross-subject statistical analysis of brain atrophy in early relapsing remitting MS patients. Proc. Int. Soc. of Magnetic Resonance in Medicine, 2625, 2003 + 2) our HBM-poster this year where we extended the above approach by using custom templates and nonparametric testing) but not to SIENAX, yet. However, you can register the GM and possibly even the WM estimates to custom templates / priors using flirt and perform such an analysis. Since it is FSL's current philosophy to use affine transformations only, you won't need the rescalings ("modulations by the Jacobian determinants") involved in SPM-driven VBM. Furthermore, Jacquline Chen has presented a method for estimating cortical thickness changes (see the siena web page http://www.fmrib.ox.ac.uk/analysis/research/siena/). Hopefully, this helps a bit.
>
> Best regards-
>
> Andreas
>
>
>
>
>
>           -----Ursprüngliche Nachricht-----
>
>
>
>
>         Von: Santiago Reig [mailto:[log in to unmask]]
> Gesendet: Fr 27.08.2004 12:05
> An: [log in to unmask]
> Cc:
> Betreff: [FSL] Regional quantification using SIENA and SIENAX
>
>
>
> 	Hi,
>
> 	I´m beginning to use SIENA and SIENAX, and I wonder if anybody has tried
> 	doing a regional analysis of volume changes. I mean getting estimates
> 	about cc of change in GM, WM or CSF for a given lobe of the brain, rather
> 	than the global PBVC. The render images are very pretty, but sometimes you
> 	need numbers to describe changes.
>
> 	Thanks in advance for any idea on this, and special thanks to Steve Smith
> 	for making FSL available. Itìs a great program!
>
> 	Santiago
>
>
> 	><((((º>`·.¸¸.·´¯`·.¸.·´¯`·...¸><((((º>`·.¸¸.·´¯`·.¸.·´¯`·...¸><((((º>
> 	 `·.¸¸.·´¯`·.¸.·´¯`·...¸><((((º>`·.¸¸.·´¯`·.¸.·´¯`·...¸><((((º>`·.¸¸.·´
> 	Santiago Reig,  PhD.
> 	   Gregorio Maranon Hospital,  Universidad Complutense de Madrid
> 	   Experimental Surgery and Medicine Lab
> 	   Dr. Esquerdo 46,  28007 Madrid, SPAIN
> 	               Fax#  34 91 426 5108, Ph#  34 91 426 5067
> 	[log in to unmask]    http://www.hggm.es/image
>
>
>

 Stephen M. Smith  DPhil
 Associate Director, FMRIB and Analysis Research Coordinator

 Oxford University Centre for Functional MRI of the Brain
 John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
 +44 (0) 1865 222726  (fax 222717)

 [log in to unmask]  http://www.fmrib.ox.ac.uk/~steve