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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