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You could do that (though it would probably be smart to check the alignment of the ROI with the FA color map in each subject). If it were me, though, I would probably figure out an ROI definition I liked (probably a 2D slice at the top of the cerebral peduncles perpendicular to the pathway, and another 2D slice at the top of what I wanted to measure, e.g. just before the corpus callosum crosses the path) and just draw it in each subject. I know some groups have worked out a tensor based registration approach, which would likely improve the alignment of white matter pathways over an FA or T1 nonlinear registration based approach to standard space, though I don’t know if this is in the cards for FSL. I would probably be more comfortable using standard space ROIs to track pathways in individual subjects if the tensors were used in the registration (note that TBSS gets around the problem of tract alignment using the skeletons, however unfortunately you can’t then deform the images using the final skeleton alignment).
Peace,
Matt.
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Miguel Burgaleta
Sent: Thursday, December 03, 2009 10:31 AM
Matt, regarding your answer -would it be reasonable to use the ROI obtained from a standard atlas as a seed mask in FDT?
Thanks
Miguel
On Thu, Dec 3, 2009 at 5:10 PM, Matt Glasser <[log in to unmask]> wrote:
Also you could use FDT to track the pathway in each subject. :)
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On BehalfOf Stephen Smith
Sent: Thursday, December 03, 2009 9:02 AM
To: [log in to unmask]Subject: Re: [FSL] defining ROI: one specific tract
Hi, you could either draw masks by hand in FSLView (start with File-
>Create-mask once you have the skeleton etc loaded in) or use one of
the standard space white matter atlases
Cheers
--------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington,
Oxford. OX3 9 DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask]
http://www.fmrib.ox.ac.uk/~steve
----------------------
On 3 Dec 2009, at 10:04, "SUBSCRIBE FSL J.Schuurman" <[log in to unmask]
> wrote:
> Hi,
>
> My question is about drawing ROIs. After running TBSS I would like
> to extract
> FA values from the internal capsule tract. If I use fslroi I can
> only select a
> rectangular ROI which often includes parts of other tracts as well.
> What is the
> best way to define a ROI containing one specific tract, without the
> involvement of adjacent tracts?
>
> Thanks,
>
> Janneke Schuurman
>
> Department of Psychiatry and Neurology
> VU University Medical Center, Amsterdam
>