Hi Doug,

This reminds me: in the dt_recon script, when bbregister is used, the gradient descent tolerance is changed (the command line includes --tol1d 1e-3 ).

I was just wondering why this happens.

Thanks!
Mike

On Tue, Jan 25, 2011 at 1:31 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
I get a file-not-found to that link, so I can't check it out. But, yes,
you should just be able to use bbregister passing it the low-b as the
template (or whatever you used at the target for motion correction). and
specifying --bold or --t2.

doug

Lena Palaniyappan wrote:
> Dear Doug & others
>
>
> The FSL page on fa to freesurfer registration (
> http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html)
> <http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html%29>  contain info
> that uses tkregister2.
>
>
>
> To determine freesurfer_to_fa space registration file, do we need to
> go through the freesurfer_to_struc and then struc_to_fa rooutine given
> in fsl pages.?
>
> I wonder if the registration can be done using the  bbregister currently.
>
> If that is the case how to get the fsl-type registration file?
> tkregister2 had an option for this but it is not working with bbregister
>
> Cheers
> Lena
> _______________________________________________________
> *Lena Palaniyappan
> *Clinical Lecturer & Honorary StR | Division of Psychiatry (
> University of Nottingham)
> South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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