Thanks for the pointers .. like I said I think I've got the directions /
grads right, but have posted you requests at:
https://www.ynic.york.ac.uk/information/visitor_files/
.. (the first 6 images are updated since my lat post)
Hope you can help (and that I understood what you wanted)
Word,
dre'
> Andre,
>
> I suspect you may have some gradient directions that need to be "flipped."
> In FSLView, load the DTIFIT_FA, the V1 according to color, and the V1
> again
> in the "lines" form. Then look at the corpus callosum in axial and
> coronal
> sections, and the corona radiata or arcuate fasciculus in sagittal
> sections.
> If you post example screenshots showing the lines in each of these
> structures clearly, I could tell you which gradient needs to be flipped,
> and
> how to do it.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Andre Gouws
> Sent: Monday, February 05, 2007 7:15 PM
> To: [log in to unmask]
> Subject: [FSL] dti processing - bedpost and probtrack
>
> Hi,
>
> Having (seemingly) succesfully created the requisite files for the dtifit
> /
> bepost processing stream (bvecs, bvals, data, nodif, nodif_brain_mask
> etc.)
> I have been trying to get to the point of down some Probtrack
> tractography.
>
> The results of my DTI_fit routines look promising (e.g. plotting dti_V1)
> and
> anatomically viable. I run bedpost on the same files that produce the
> 'promising' dti-fit results (I paralellise this across my Quad Mac G5) and
> everything seems to run smoothly (takes about 4 hours for a 128x128x45
> 2x2x3mm volume) ..
>
> However, when I try tractography (with default parameters and some other
> variations suggested on this mail list) none of my tracts are ever longer
> than a couple of centimeters (?) .. even when seeding in regions od high
> FA
> which other streamlining routines find long pathways for ... (GE's
> proprietary software, dodti, my own streamlinign routines in python/vtk)
> ..
>
> I looked back at the quality of the dyadic_vectors (representing the PDD?)
> file and it seems to be 'worse' / less uniform than the original dti_V1.
>
> I have some examples available for viewing at
>
> https://www.ynic.york.ac.uk/information/visitor_files
>
> So .. in short .. why are my tractography results so poor .. surely if I
> seed in some areas of high FA (CC, cingulum, etc) I should find some
> longer
> paths? ..
>
> I have looked at the vector directions and think I am applying them
> correctly .. but may be wrong ..
>
> Thanks for your time
>
> Andre'
>
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