Hi -
The problem is that your nodif_brain_mask is not binary.
Voxels only get processed if the voxel value in nodif_brain_mask is a 1.
if you do
avwmaths nodif_brain_mask -bin nodif_brain_mask
then redo the dtifit, all should be well.
T
On Fri, 5 Aug 2005, Jon Chia wrote:
> Hi Tim,
>
> Thank you so much for your help. I've uploaded
> my input directory. The reference number is
> 842490. Thanks again.
>
> Regards,
> Jon
>
>
>
> On Fri, 5 Aug 2005 09:35:00 +0100, Tim Behrens <[log in to unmask]> wrote:
>
> >Jon -
> >I'm not sure what this is - can you tar up the input directory
> >
> >tar cvf problems.tar <inputdir>
> >gzip --best problems.tar
> >
> >and upload it onto our server
> >
> >(go to http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi and follow
> >instructions - send me the crucial nummber!!)
> >
> >Then I'll have a look
> >
> >Thanks
> >
> >Tim
> >
> >
> >
> >On Thu, 4 Aug 2005, Jon Chia wrote:
> >
> >> Hi,
> >>
> >> The dtifit now runs, but my results are just
> >> partial edges of the brain. The BET nodiff_brain_mask
> >> I use is the b0 image of the DTI sequence. I've attached
> >> what it looks like.
> >>
> >> I am assuming it may still have something to do with my
> >> bvecs file which I think I've normalized and think I've
> >> filled out correctly. What could be my problem? Thanks.
> >>
> >> Regards,
> >> Jon Chia
> >>
> >
> >--
> >-------------------------------------------------------------------------------
> >Tim Behrens
> >Centre for Functional MRI of the Brain
> >The John Radcliffe Hospital
> >Headley Way Oxford OX3 9DU
> >Oxford University
> >Work 01865 222782
> >Mobile 07980 884537
> >-------------------------------------------------------------------------------
> >=========================================================================
>
--
-------------------------------------------------------------------------------
Tim Behrens
Centre for Functional MRI of the Brain
The John Radcliffe Hospital
Headley Way Oxford OX3 9DU
Oxford University
Work 01865 222782
Mobile 07980 884537
-------------------------------------------------------------------------------
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