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
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