Thanks gents .. I'll Try this tonight

after all .. sleep is over-rated
> 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>
> ---------------------------------------------------------------------------
>