Hi there -
This result is exactly as it should be. If you overlay this onto the
seed-space image (e.g the FA map if you ran the tracking in diffusion
space), and change the colour scale on the overlay to "red-> yellow",
it will look just like it does in the manual.
There are instructions for doing this in fslview here:
http://www.fmrib.ox.ac.uk/fsl/fslview/index.html
Cheers
T
Tim Behrens
Centre for Functional MRI of the Brain
The John Radcliffe Hospital
Headley Way Oxford OX3 9DU
Oxford University
Work 01865 222782
Mobile 07980 884537
[log in to unmask]
www.fmrib.ox.ac.uk/~behrens
On 28 Jun 2006, at 16:06, Hesamoddin Jahanian wrote:
> Hi there
>
> You are right, Bedpost had done its job. How ever I do not know
> what was the
> reason for the error message.
> After that, I tried the single seed tractography but the result was
> different from what has been displayed in help file.
> I mean I just got a file in which the tracts were displayed as gray
> levels
> without any back ground. (it is attached to this email)
> How can I show the tracts in different color (red for example)
> overlaid on
> FA map as background?
>
> cheers
>
> Hesam
>
>
>
> On Mon, 26 Jun 2006 17:57:16 +0100, Tim Behrens
> <[log in to unmask]> wrote:
>
>> It looks like bedpost has worked ok.
>>
>> Can you describe the probtrack problem more extensively?
>>
>> Cheers
>>
>> T
>>
>>
>> Tim Behrens
>> Centre for Functional MRI of the Brain
>> The John Radcliffe Hospital
>> Headley Way Oxford OX3 9DU
>> Oxford University
>> Work 01865 222782
>> Mobile 07980 884537
>>
>> [log in to unmask]
>> www.fmrib.ox.ac.uk/~behrens
>>
>>
>>
>>
>>
>> On 26 Jun 2006, at 17:26, Hesamoddin Jahanian wrote:
>>
>>> Hi
>>>
>>> Thank you very much!
>>> Yeah that was a problem. I add a caraige return and the bedpost
>>> staretd to
>>> analyze but after 24 hrs I recieved this error message:
>>>
>>> Errors: /home/.../FSL/bin/bedpost: line 293: syntax error:
>>> unexpected end of
>>> file.
>>>
>>> but the .bedpost folder is created and all the files
>>> (dyadic_vectors.nii.gz,
>>> mean_fsamples.nii.gz, mean_phsamples.nii.gz, mean_thsamples.nii.gz,
>>> merged_fsamples.nii.gz, merged_phsamples.nii.gz,
>>> merged_thsamples.nii.gz)
>>> are generated.
>>>
>>> The thing is that when I run "ProbTrack" it does not detect any
>>> fiber.
>>>
>>> do you have any idea what the problem is?
>>>
>>>
>>> BTW, these are the outputs that I got:
>>>
>>> making bedpost directory
>>> copying files to bedpost directory
>>> processing data on local host
>>> 0 slices processed
>>> .
>>> .
>>> .
>>> 42 slices processed
>>> 43 slices processed
>>> Merging outputs into 4D files
>>> DONE
>>> <=============== I recived the error message at thhis
>>> point
>>> Done!
>>>
>> =====================================================================
>> ====
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