Hi Saad, could you explain a bit more in detail how to proceed.
When I run probtrackx with and without the --pd option I have the two
probabilistic tracking distributions - how do I get from them the expected path length?
Would it work like this?
fslmaths corrected_path_distribution.nii.gz -div uncorrected_path_distribution.nii.gz pathlength.nii.gz
> (make sure you use waypoint and stopping mask to select the tract of interest)
Why is that so important? For testing I used a single voxel as seed and this seemed to work.
However what are the reasons for using waypoint and stopping mask?
> plot FA etc. as a function of expected distance (it will be a cloud of voxels that you could re-bin according to distance).
How would I do this? I suppose there is a simple matlab command?
Thanks, Michael
On 29.01.2010, at 13:20, Martin Kavec wrote:
> Hi Saad,
>
> makes a lot of sense. I'll certainly give it a try, to see what it gives in
> reality. However, this is only applicable to the tracks, which do not branch.
>
> cheers,
>
> Martin
>
> On Friday 29 January 2010 12:10:54 Saad Jbabdi wrote:
>> 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.
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