Hi Mike,
What do you mean exactly when you say that "FSL has trouble viewing the colormaps"?
You need to make sure that you can visualise V1 (output of dtifit) correctly in fslview (using line-mode), ensuring that the orientation of V1 represents sensible-looking white matter trajectories. Otherwise, the rest of the analysis (bedpostx, probtrackx) will produce incorrect results. In general, it is a matter of changing the bvecs file by either flipping one of the coordinates, or swapping coordinates.
Your second problem is more puzzling. Is it possible that your termination mask might also contain your seed mask? Can you run it just with the seed and see what you get?
Cheers,
Saad.
On 25 Aug 2010, at 19:59, Michael Yassa wrote:
> Hello all,
>
> I have been acquiring coronal 0.6 mm in-plane DTI scans of the hippocampus and surrounding cortex. I have been able to use FSL to calculate the tensors on this data and calculate my scalar maps (although FSL has trouble viewing the colormaps on this coronal data for some reason).
>
> I would like to do probabilistic tractography to see if I can map the connectivity between two diffusion-space seed ROIs. I used bedpostx first and got all of the appropriate output files. Then I tried to apply probtrackx with a single mask (seed ROI) setting the termination zone to by another mask (target ROI). Everything runs fine, however my fdt_paths file essentially is identical to my seed mask file (except the value is equivalent to the number of samples I set, e.g. 1000). I've done this a few ways using the termination mask as a waypoint and the result is always the same.
>
> I thought that perhaps since my voxel size is small, I should change the step size to something more appropriate (0.2), but I do have anisotropic slices (thickness = 3 mm). Not sure how to proceed.
>
> Any thoughts you have on this would be greatly appreciated.
>
> Thanks so much.
>
> Best,
>
> Mike
>
>
> --
> Michael A. Yassa, Ph.D.
> Assistant Professor in Psychological and Brain Sciences
> Johns Hopkins School of Arts and Sciences
> 3400 N. Charles Street, Ames Hall
> Baltimore, MD 21218
> Tel: (410) 516-7055; Fax: (410) 516-4478
> Email: [log in to unmask]
> Web: http://pbs.jhu.edu/research/yassa/
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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