thanks Saad, you were right my y-coordinates were flipped. I figured  
that out since in the occipital callosal fibers the tensors were  
looking from anterior-lateral to posterior-medial instead from  
anterior-medial to posterior-lateral.
However I had some issues with wrong bvecs already in the past - so I  
am wondering: Do you have an approach on how to check you have the  
right bvecs?
E.g. we correct for angulation to ac-pc-line - it's mostly only some  
degrees but for tracking it will matter I guess.
1) Would you discourage to angulate to ac-pc on acquistion as an extra  
uncertainty factor?
2) How do you make yourself confident that you're working with the  
right bvecs - any quick test for it?

cheers, michael



On 28-Nov-08, at 1:13 AM, Saad Jbabdi wrote:

> 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