Hey Guys,
I wonder if that's possible that given FSL use a very permissive angle threshold your tract are going back and forth from A to B and B to A and then A to B again (to finally stop in B).
BTW I received nat. neuro this morning Saad. Nice first page ;)
Best
michel
On 17 Feb 2012, at 09:33, romain valabregue wrote:
> Hello
>
> We have a the same problem : we want the part of the track that only goes between 2 region A and B
> So if we choose a seed in A and a waypoint+termination in B we also get fiber part that go through A in the opposite direction.
> My understanding is that it is due to the fact that fsl track a fiber in 2 direction and consider it as the same fiber
> So starting from A in one direction it comes to B and stop but in the other direction it goes where it wants
> Is that right ?
>
> The solution to add an extra exclusion mask in the opposite direction is not very easy and can not be 100% efficacy ...
>
> An easier solution would be to construct a fiber in only one direction. Then we will easily get rid of the fiber part that goes in the opposite direction since the opposite part will never enter in B.
> Is there a way to restrict fsl fiber tracking in only one direction ?
>
> Thanks for your help (and for this nice software).
>
> Romain
>
>
> Le 27/12/2011 13:58, Saad Jbabdi a écrit :
>> Hi Volker
>> If you are using B as termination, you should not see streamlines running out of B. It is more likely that these streamlines go past B without intersecting it, then come back to terminate in B.
>> An easy way around this is to have an exclusion mask past B. In your case, track from prefrontal, terminate+waypoint at Amygdala, and add an exclusion mask e.g. a single plane caudal to the Amygdala.
>>
>> Cheers,
>> Saad
>>
>>
>>
>> On 22 Dec 2011, at 13:20, Volker Baur wrote:
>>
>>> Dear FSL experts,
>>>
>>> we are running probtrackx to do tractography between two ROIs A and B. We are only interested in the direct connection between A and B, so tried to use A as seed and B as termination mask. The problem is that there are still fibers running out of B into the opposite direction of A. Also we tried to use A as seed and B as waypoint AND termination mask. Has anyone an idea of which would be the best way to obtain only those fibers that are exactly between the two ROIs? For example, if we want to map tracts between a prefrontal ROI and amygdala, we are not interested in fibers running out of the amygdala to the occipital cortex.
>>>
>>> Also, is there a rationale of which of the two ROIs using as seed and which as termination mask?
>>>
>>> Thanks very much for any help,
>>> Volker
>>>
>> --
>> Saad Jbabdi
>> University of Oxford, FMRIB Centre
>>
>> JR Hospital, Headington, OX3 9DU, UK
>> (+44)1865-222466 (fax 717)
>> www.fmrib.ox.ac.uk/~saad
>>
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