Hi Sunita,
Yes, when you flip the image, you need to adjust your bvecs accordingly.
I'd recommend checking that you get the correct orientation by looking
at your vector map once you run dtifit, as anything weird will pop
right out (that will save you time before running bedpostX and
probtrackX).
Best,
Cherif
------------------------------------------------------------------------------------------
Cherif P. Sahyoun HST-MEMP
Developmental Neuroimaging of Cognitive Functions
C: 617 688 8048
H: 617 424 6956
[log in to unmask]
"Live as if this were your last day. Learn as if you'll live forever"
Ghandi
-------------------------------------------------------------------------------------------
On Thu, Oct 30, 2008 at 8:08 PM, Sunita Bava <[log in to unmask]> wrote:
> Hello all,
>
> In running probtrackx, we find that that the generated paths are not in the
> correct orientation. Our input data consists of a preprocessed dataset
> (using both AFNI and FSL tools) that is in nifti format. In order for the
> dataset to be correctly oriented and to appear accurately in the viewer we
> ran the following commands before running bedpostx:
>
> fslorient -swaporient data.nii.gz
> fslswapdim data.nii.gz x -y z data.nii.gz
>
> As the resulting fiber paths from probtrackx were incorrectly oriented, the
> commands above were applied to the fdt.paths file, but still did not result
> in a correct overlay. We are wondering what the issue is here. Does the
> bvecs file need to be adjusted to account for the changes in orientation
> that were applied to to the diffusion dataset? Your assistance is much
> appreciated.
>
> best,
> Sunita
>
|