Hi Julia,
we'll try!
Thanks,
Jan
On 08/31/2014 05:41 PM, Owen, Julia wrote:
> If you're dealing with streamlines leaking across the interhemispheric fissure, an automatic way that was worked for me is to create an exclusion or termination mask computed by FA<0.1. You may have to play with the threshold, but this creates a mask that fills in the fissure and all around the surface of the brain. This won't stop streamlines from erroneously crossing deeper within the brain, of course.
>
> -Julia
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Jan Schreiber [[log in to unmask]]
> Sent: Friday, August 29, 2014 9:11 AM
> To: [log in to unmask]
> Subject: Re: [FSL] probtrackx2: jumps across hemispheres --usef
>
> Thanks Saad!
>
> On 08/29/2014 02:39 PM, Saad Jbabdi wrote:
>> Hi-
>>
>> You can use a mid-sagittal plane as an exclusion mask (but exclude the
>> commissures from that mask).
>>
>> Cheers
>> Saad
>>
>>
>> On 29 Aug 2014, at 13:20, Jan Schreiber <[log in to unmask]
>> <mailto:[log in to unmask]>> wrote:
>>
>>> Dear FSL experts,
>>>
>>> we are using probtrackx2 for probabilistic tractography.
>>> In some subjects (5 out of 50) some of the tracks seem to cross the
>>> hemispheres outside the Corpus Callosum / Anterior Commisure /
>>> Posterior Commisure.
>>>
>>> Do you have an idea how we could prevent that?
>>>
>>> There are no obvious artefacts visible in the data.
>>> We tried to use the --usef option but it restricts tractography to the
>>> seed regions.
>>>
>>> Would it make sense to use a white matter instead of brain mask?
>>>
>>> Thanks,
>>> Jan
>>>
>>
>> ------------------------------------------------------------------
>> Saad Jbabdi, PhD
>> MRC Career Development Fellow &
>> University Research Lecturer
>>
>> FMRIB Centre, University of Oxford,
>> John Radcliffe Hospital, Oxford, OX3 9DU, UK.
>> tel (+44)1865-222466 (fax 717)
>> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
>> <http://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi>
>>
>>
>>
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