Hi
Here is a simpler alternative:
- run probtrackx with and without --pd to get expected path length
(make sure you use waypoint and stopping mask to select the tract of
interest)
- plot FA etc. as a function of expected distance (it will be a cloud
of voxels that you could re-bin according to distance).
The only thing is that when comparing different subjects, you want to
make sure you take these measurements along the same tracts, and avoid
noisy data points from alternative routes that are not common across
subjects, but you can solve that by looking only at the overlapping
voxels across subjects in some common space.
Does this make sense?
Cheers,
Saad.
On 29 Jan 2010, at 10:58, Martin Kavec wrote:
> I thought about another alternative approach: flow propaggation.
> This is used
> in vessel tracking. The flow front wave would propagate through our
> track and
> integrate the FA accross its crossection. This should be possible to
> program
> in VTK (Visualization Toolkit), which is anyway part of the FSL
> distribution,
> because it is used in fslview. Anybody from the fslview developers
> would like
> to add an idea?
>
> cheers,
>
> Martin
>
>
> On Thursday 28 January 2010 19:29:40 Matt Glasser wrote:
>> I had more thoughts about a general solution for this as well
>> (don't know
>> how much would be possible):
>>
>> 1) Feed a thresholded pathway into tbssskeleton and hope it spits
>> out the
>> core of highest intensity.
>> 2) Determine the plane perpendicular to this core at each point
>> along its
>> length and the angles between this perpendicular plane and the three
>> orthogonal planes that make up the original image.
>> 3) Take the thresholded mask of the pathway and transform it
>> according the
>> angles above (make a flirt matrix with the appropriate angles, and
>> apply
>> it) so that the perpendicular plane is now parallel to the xy
>> plane, and
>> then select the slice of interest.
>> 4) Resample this slice back onto the original image (use it as the
>> reference image and apply an identity transform with flirt)
>> 5) Measure the quantitative parameter of interest using this
>> resampled
>> slice mask.
>> 6) Repeat steps 2-5 for all points along the length of the core.
>>
>> I think this would be a really useful capability for a lot of
>> applications.
>> I feel like step 2 is probably the hardest in that I can't think of
>> a way
>> to do it with FSL tools.
>>
>> Any improvements to the above would be most appreciated.
>>
>> Peace,
>>
>> Matt.
>
--
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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