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.

-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Michael Scheel
Sent: Thursday, January 28, 2010 8:25 AM
To: [log in to unmask]
Subject: Re: [FSL] FA along a track

Hi Martin, could you comment a little more of what you've done so far.
Do you have individual CST masks already? Or would you rather use an atlas
based approach?

My first idea that would be possible in a shell script is the following:
1) run tbss on your datasets with FMRIB58 as target - this will create an
appropriate 4d file
2) take the atlas mask for cst in the mask
3) split the mask into it's slices with fslsplit
4) run a loop with fslmeants (using the mask option) for each slice of the
mask
this would create FA along z-directions ,wich should not be too far away
from 'tracking along CST'
This will of course work on other tracts as well as long their orientation
is similar to the x,y or z direction.
The validity of this approach would be greatly depend on the initial
registration. However the advantage I see is that this will be relatively
easy to accomplish in a script.

As I'm trying to do something similar I would be more than happy for having
a look at your data.

Other ideas and comments especially towards moving along the tract center
and averaging the voxels in a perpendicular plane to the tract?

cheers, michael

On 27.01.2010, at 20:56, Martin Kavec wrote:

> Hi Michael,
>
> yeah exactly. I was struggling to send the image to the mailing list, but
it
> was too big. That is exactly what I want. I know DTIStudio of Susumu Mori
can
> give this profile, but I don't know how he does that.
>
> Although with cortico spinal track it is rather easy to go through slice
> direction, I am interested in more general solution, because the track of
my
> interest is rather curvy. If you would take this approach with SLF you
would
> mix FAs from rather distinct anatomical locations. Therefore something
more
> tricky should be used. Something as David just suggested - strightening
the
> track, but how to do it practically?
>
> Thanks,
>
> Martin
>
> On Wednesday 27 January 2010 20:42:46 Michael Scheel wrote:
>> Hi Martin,
>>
>> I've seen the paper by Sage et al. Quantitative diffusion tensor imaging
in
>> amyotrophic lateral sclerosis: Revisited See screenshot attached - is
this
>> what you want? I'd be interested in how to do this with fsl tools as
well.
>>
>> cheers, michael