Hi,
A stop mask simply stops paths that pass through it. A waypoint mask
requires all samples to pass through it, and would be part of a unsymmetric
two ROI approach.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Nobukatsu Sawamoto
Sent: Wednesday, October 31, 2007 9:26 PM
To: [log in to unmask]
Subject: Re: [FSL] ProbTrack problem with symmetric masks (extraneous
fibres)
Hi,
I am just wondering the reason to specify waypoint mask as well as stop
mask. So, what is the advantage of adding waypoint mask? Why stop mask
only is not enough?
Many thanks in advance!
Nobu
Kyoto University
>and also to --avoid="something" (without this, I still manage to
>see a lot of clever fibers that find altrnate pathways to the
>sides the must not arrive ;)
>
>Naj
>
>
>On Tue, 30 Oct 2007, David Gutman wrote:
>
>> Yes-- I had a similar issue-- to isolate a specific path you also need
to
>> specify a --stop option, or at least this seems to have worked for me.
>>
>>
>> >From what I was able to discern, it appears if you just specify
a "Waypoint"
>> (which is essentially what the two way symmetric mode does) then it
keeps
>> all fibers that go from "A" to "B" but then the fiber will continue on,
>> leading to seemingly extraneous paths. What I had done is to specify
both a
>> waypoint (--waypoints option) and a stop mask (--stop )and use the same
>> mask for both--
>>
>> Something like this..
>>
>> /usr/share/fsl/bin/probtrackx --mode=seedmask --seed=$SEED_MASK
>> --stop=$TARGET_MASK --waypoints=$TARGET_MASKS
>>
>> should work (of course you need all the other probtrackx syntax as well
or
>> just use the GUI).
>>
>> dg
>>
>>
>>
>> DG
>>
>>
>> On 10/29/07, Clare Emily Bajraszewski
<[log in to unmask]>
>> wrote:
>> >
>> > Hi everyone,
>> >
>> > I have been using a dual-region-of-interest approach (2 masks-
symmetric on
>> > FDT, with one mask in the primary visual cortex and another in the
>> > anterior optic radiation) to track the optic radiations on each side,
but
>> > many tracts have been included that are not between the 2 masks.
>> >
>> > e.g. tracts crossing the midline, and tracts heading anteriorly to the
>> > frontal lobe- these are clearly not part of the optic radiations.
>> >
>> > Has anyone else had this problem and can anyone help?
>> >
>> > Many thanks!
>> >
>> > Clare Bajraszewski (Howard Florey Institute)
>> >
>>
>>
>>
>> --
>> David A Gutman, M.D. Ph.D.
>> Department of Psychiatry & Behavioral Sciences
>> Emory University School of Medicine
>>
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