Andre,
Your bvals file should say 0 1000 1000 ... rather than 0 1 1 as it does now
(assuming your b value was 1000).
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Andre Gouws
Sent: Wednesday, February 07, 2007 10:49 AM
To: [log in to unmask]
Subject: Re: [FSL] dti processing - bedpost and probtrack
I have tried to uploaded my bedpost and dti_fit directories (with all
original files) to upload number:* 695345*.
I think they may be too large (the upload seemed to stall)
I can just upload the raw data but thought it might save some time to
have the full processing stream available.
I have made the directories available for download (155MB) at:
https://www.ynic.york.ac.uk/~andre/YNIC_processing.tar.gz
Let me know if I should upload smaller files / folders without the
processing
Thanks again
Andre'
Saad Jbabdi wrote:
Hi - This is strange. The V1 vectors look Ok, but the dyads are not
smooth. As these vectors represent the mean of the local orientation
distribution, this might indicate that these distributions are too wide
(uncertain), even in highly anisotropic white matter (which explains why
you get short tracts). This can be due to a low snr, but your images
look fine.
You can upload your data here: www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
Give us the upload number, and we can have a look.
Cheers,
Saad.
On 7 Feb 2007, at 01:03, Andre Gouws wrote:
> 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] <mailto:[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'
>>
---------------------------------------------------------------------------
Saad Jbabdi, Postdoctoral Research Assistant, Oxford University FMRIB
Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222545 (fax 222717)
[log in to unmask] <mailto:[log in to unmask]>
http://www.fmrib.ox.ac.uk/~saad <http://www.fmrib.ox.ac.uk/%7Esaad>
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