2008/1/18, Gwenaëlle DOUAUD <[log in to unmask]>:

Hi Ling,

basically, your two images are far too different: your
T1w has a lot of neck in it compared with the bo etc.
You should bet both images first.
I've checked and it's working with your T1w image
being betted with -f 0.3, the b0 with -f 0.2. If you
want the whole b0 to be registered to the T1, then you
need to output the flirt matrix (-pmat) and to apply
it to your entire bo (-init b0_brain_t0_t1_brain.mat
-applyxfm).

Hope this helps,
Gwenaelle

--- "Wang, Ling" <[log in to unmask]> a écrit :

> Dear FSL Experts,
>
> I met a problem with flirt. When I used flirt to
> register the dti data (e.g.,
> the B0 image) to t1 image, I found the outputted
> image is not correct (its
> orientation is totally changed). The command
> outputted by flirt is :
> flirt -in /daten/Reg/B0_first.nii.gz -ref
> /daten/Reg/t1.nii.gz -out
> /daten/Reg/B0_first_t1.nii.gz -omat
> /daten/Reg/B0_first_t1.mat -bins 256
> -cost mutualinfo -searchrx -180 180 -searchry -180
> 180 -searchrz -180 180
> -dof 12  -interp trilinear
>
> However, I met this problem only for some subjects'
> data, other data are
> fine with flirt.
>
> I have uploaded the images I used to
> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi, and
> the number of the upload
> session is 846956.
> Could please so kindly have a look on that? Thank
> you very much in advance!
>
> Best wishes,
> Ling Wang
>
> --
> Ling Wang
> Cognitive Neurology
> Institute of Neuroscience and Biophysics - Medicine
> Research Centre Juelich
> 52425 Juelich, Germany
> phone:  +49-2461-618609
> Fax:     +49-2461-612820
>

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