Hi Saad and Matt,
thanks for your answers and sorry for the replicate question. I just had not
seen Matt's answer - sorry about that.
Thanks Michael
On Wed, 15 Oct 2008 22:33:52 +0100, Saad Jbabdi <[log in to unmask]> wrote:
>Hi Michael,
>
>As Matt said, the burnin is related to bedpostx, where the
>distribution of local orientations is estimated from the data. The
>burnin period serves for the algorithm to stabilise before sampling
>from the distribution on orientations. bedpostx creates 50 samples in
>each voxel by default.
>the 5000 samples are related to probtrackx (not bedpostx), where the
>bedpostx samples are used repeatedly to sample connections (5000
>samples by default per voxel in the seed mask).
>
>Cheers,
>Saad.
>
>On 15 Oct 2008, at 21:37, Michael Scheel wrote:
>
>> Hi Saad,
>>
>> thanks for the 3D tool hint - I will give it try. Do you know about
>> the
>> Burnin Option and how it relates to the total-number-of-samples-
>> generated in
>> the Brigde 2008 paper where you have been coauthoring.
>>
>> Michael
>>
>>
>> On Wed, 15 Oct 2008 09:13:36 +0100, Saad Jbabdi
>> <[log in to unmask]> wrote:
>>
>>> Hi - The 3D tract figure was made with Anatomist, which is part of
>>> the
>>> BrainVISA software. But this was prior to the 3D tools in fslview, so
>>> maybe you could obtain similarish results with fslview?
>>>
>>> Saad.
>>>
>>>
>>> On 15 Oct 2008, at 02:22, Michael Scheel wrote:
>>>
>>>> Hi,
>>>>
>>>> i have a short question regarding FDT and number-of-sampling /
>>>> Burnin-Option. I just read the Bridge 2008 paper "Changes in
>>>> connectivity after visual cortical brain damage underlie altered
>>>> visual function"
>>>> and was wondering if the total-number-of-samples-generated
>>>> mentioned (5000 in this paper) is equivalent to the Burnin option
>>>> (default 1000) in BedpostX or if these are different things.
>>>>
>>>> Second question: could someone point me to a tool doing a 3d-tract
>>>> visualization similar to the one in this paper.
>>>>
>>>> Thanks, Michael
>>>>
>>>
>>> ---------------------------------------------------------------------------
>>> 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] http://www.fmrib.ox.ac.uk/~saad
>>> ---------------------------------------------------------------------------
>>
>
>---------------------------------------------------------------------------
>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] http://www.fmrib.ox.ac.uk/~saad
>---------------------------------------------------------------------------
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