Hi Ting,
I hope I can provide some help until the experts come on. Since these
voxel coordinates are in standard space, did you register all of your
diffusion data (with the fdt registration toolbox) to the MNI brain
and then run probtrack? When you load the data_brain.nii.gz that has
been moved to standard space in FSLView, does it look like there was
good overlap with the MNI brain?
ted
On Jun 24, 2008, at 4:59 AM, SUBSCRIBE FSL Ting-Shuo Yo wrote:
> Hi,
>
> I am tring to use the PROBTRACKX in FDT, and I have encountered
> some strange
> results. I hope some experienced FSL users can help me figure out
> the problem.
>
> I have prepared my diffusion dataset with 7 b0 images in the begining,
> following by 60 gradient images. The "bvecs" and "bvals" are
> specified in
> the same order, and the results of DTIFIT seem fine (compared to
> other DTI
> tools).
>
> After running BEDPOSTX, I use two voxel points (one in gcc and the
> other in
> scc) as the seeds, but the results seems a bit strange: the
> connectivity
> distribution do not follow exactly the tensor orientation (to bend
> forward
> in gcc and backward in scc), but go across the ventricles. The
> results
> contradict to other fiber tracking tools, and I hope someone can
> help me
> find out the mistake I have made.
> (please see the pictures at:
> http://lh5.ggpht.com/tingshuo.yo/SGCvyHfEQyI/AAAAAAAACkM/
> WX436W1SvNc/fsl_probtrackx_01.jpg
> http://lh5.ggpht.com/tingshuo.yo/SGCvyLtIahI/AAAAAAAACkU/
> Z0dtkdZrBLc/fsl_probtrackx_02.jpg)
>
> Following is the command I used:
>
>> probtrackx --mode=simple --seedref=data.bedpostX/nodif_brain_mask -o
> results -x seed.cc -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --
> forcedir
> --opd -s data.bedpostX/merged -m data.bedpostX/nodif_brain_mask --
> dir=results
>
> In the file seed.cc, only two lines specifying the voxel position
> of gcc(46
> 82 46) and scc(46 45 46).
>
> Thanks in advance.
>
>
> Ting
>
> =============================================================
> Ting-Shuo Yo
>
> Max Planck Institute for Human Cognitive and Brain Sciences
>
> E-mail: [log in to unmask]
> =============================================================
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