Hi Andreas,
It is hard to keep both. I think that the wise thing to do here is to
make a termination mask stop a track as soon as it enters it, as it
should do. Then in special cases, such as two-masks tractography, I
guess this has to be dealt with by running tractography twice.
Cheers,
Saad.
On 8 Apr 2009, at 22:57, Andreas Bartsch wrote:
> Hi Saad,
>
> couldn't we keep both options? They both seem to make sense -
> depending on the objective.
> Cheers-
> Andreas
> ________________________________________
> Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag
> von Saad Jbabdi [[log in to unmask]]
> Gesendet: Mittwoch, 8. April 2009 10:59
> An: [log in to unmask]
> Betreff: Re: [FSL] Termination masks
>
> Hi Catherine,
>
> You are right (and I was in July 2008!), the tracts will stop as soon
> as they leave the termination mask (which still contradicts the
> website).
>
> The reason I had originally done this was to be able, in two-masks
> tractography, to make your seed masks as termination mask. So seeding
> from one of them, you wouldn't stop until you are out. It is
> convenient in that case, but obviously not in other cases such as
> yours.
>
> I have corrected that now, so tracts will stop when they enter the
> termination mask (was meant to do it a long time ago!).
> This will be included in the next patch. In the mean time, I could
> either send you a compiled version of probtrackx, or tell you where to
> change the code if you want to compile it yourself.
> Sorry for the confusion,
>
> Saad.
>
> On 8 Apr 2009, at 09:36, Catherine Traynor wrote:
>
>> Hi Saad and Dianne
>>
>> I've have tried using FSL4.0.4 and FSL1.1.1, and for both versions
>> if i use
>> a termination mask paths are only stopped when they leave the mask.
>>
>> This result agrees with the response to an earlier query from Junichi
>> Chikazoe (Re: Termination mask, 2 Jul 2008), but is not what it says
>> on the
>> FSL website ("Pathways will be terminated as soon as they enter the
>> termination mask").
>>
>> Has the probtrackx code been updated since Jul '08 to ensure that
>> paths are
>> terminated when they enter the termination mask?
>>
>>
>> Thanks, Catherine
>>
>
> Saad Jbabdi
> Oxford University FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> +44 (0) 1865 222545 (fax 717)
> www.fmrib.ox.ac.uk/~saad
>
Saad Jbabdi
Oxford University FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
+44 (0) 1865 222545 (fax 717)
www.fmrib.ox.ac.uk/~saad
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