[Mrtrix-discussion] Inverted z-gradients

Donald Tournier d.tournier at brain.org.au
Tue Jul 31 16:54:18 PDT 2012


Hi Peter,

I assume you supplied the gradient directions manually, rather than having
MRtrix read them straight from the DICOM headers? If not, then that would
be a bug that I'd need to fix. But otherwise, yes, there is no simple way
to change the sign of the gradients on the command line, but it should be
pretty straightforward to load the file in matlab and do it there, or write
a tiny python script to do it.

By the way, if you do supply the directions manually, be aware that the
directions in MRtrix are assumed to be provided with respect to
real-world/scanner coordinates, not the image axes as is usually the case
for FSL and others. This will cause issues if your images are not acquired
as straight axials.

Cheers,

Donald.


On 31 July 2012 22:58, Peter Neher <p.neher at dkfz-heidelberg.de> wrote:

> Dear all,
>
> I am having some trouble with my tensor reconstruction. There seems to be
> a sign issue with the z-component of the gradients directions. Is it
> possible to correct this with any command line option or do I have to
> directly change the sign in the gradient encoding file?
>
> Best
> Peter
>
> --
> Dipl.-Inform. Peter Neher
> German Cancer Research Centre
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> Stiftung des öffentlichen Rechts)
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-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9035 7033
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