Hi Michael,
I suspect this is a problem with your bvecs orientations. Even when
the colour coded V1 image looks fine, there can still be a sign flip
in either the x, y or z component of V1 (which in turn can be due to a
flip in the same component of bvecs).
So in order to ensure that this is not the case, you need to look at
V1 in "line mode" in fslview (not RGB mode), and make sure that e.g.
the corpus callosum runs fine on both coronal and axial views.
Cheers,
Saad.
On 27 Nov 2008, at 18:06, Michael Scheel wrote:
> Hi everybody,
>
> I have a question regarding the meanf2samples.nii.gz output of
> bedpostx. As i understand it shows in which voxels the data support
> a second fibre orientation. I have been looking at my data and
> compared them to the data in the tbss practical dataset. At first I
> was very happy since it seems that the data support a lot of second
> fibre orientation.
> But when I use probtrackx on the dataset I just don't get reliably
> tracking. Even V17-left-right connections (with Callosum as
> waypoint) I don't get any results. I checked on the tutorial-data
> set - where it runs fine and gives expected results. Therefore I
> think that that the problem lies in the data. (my data have 32
> directions, b-value 700, 3 averages - dtfit works excellent with
> good FA and correct color coding - so bvals/bvecs should be ok as
> well)
> Any idea what's going on? Is the meanf2samples.nii.gz showing that
> my data is too noisy?
>
> Thanks a lot, Michael.
>
Saad Jbabdi
Oxford University FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
+44 (0) 1865 222545 (fax 717)
www.fmrib.ox.ac.uk/~saad
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