You need to load the diffusion vectors as lines in FSLView and check in each
plane that they match reasonable anatomy. If there is a problem, you will
find that in two of the three planes they do not match the anatomy. It is
the axis that is common to these planes (but not to the one that is correct)
that needs to be flipped.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Nurunisa Neyzi
Sent: Friday, July 13, 2007 7:38 PM
To: [log in to unmask]
Subject: Re: [FSL] dtifit problem
Hi thanks, it worked. One final question. I was not sure whether my
gradients had the right direction. So I changed their signs along x
and then along y (made all the - to + and vice versa). I get the exact
same results. Is this normal?
On 7/13/07, Matt <[log in to unmask]> wrote:
> Make sure you have a carriage return at the end of your bvecs and bvals
> files.
>
> Peace,
>
> Matt.
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Nurunisa Neyzi
> Sent: Friday, July 13, 2007 6:46 PM
> To: [log in to unmask]
> Subject: Re: [FSL] dtifit problem
>
> Hi thanks- I did and I had a spacing problem in bvecs. Now I corrected
> that, I still get empty FA maps. I checked the orientation
> (radiological). And I cannot think of what might be going wrong. tx!
>
> On 7/13/07, Matt <[log in to unmask]> wrote:
> > Try running bedpost_datacheck to make sure your files are in good order.
> >
> > Peace,
> >
> > Matt.
> >
> > -----Original Message-----
> > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
Behalf
> > Of Nurunisa Neyzi
> > Sent: Friday, July 13, 2007 5:04 PM
> > To: [log in to unmask]
> > Subject: [FSL] dtifit problem
> >
> > Hi when I try to run the dtifit,
> >
> > dtifit -k ALLDTI_EddyCor.nii.gz -m nodif_brain_mask.nii.gz -o out -b
> > bvals -r bvecs
> >
> > I got an error that says
> >
> > terminate called after throwing an instance of 'NEWMAT::IndexException'
> > Abort
> >
> > I never had this before, what could be going wrong?
> >
> > tx, nurunisa
> >
>
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