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 Hopefully, this helps a bit. 

Best regards- 




          -----Ursprüngliche Nachricht----- 


        Von: Santiago Reig [mailto:[log in to unmask]] 
Gesendet: Fr 27.08.2004 12:05 
An: [log in to unmask] 
Betreff: [FSL] Regional quantification using SIENA and SIENAX

	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 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
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