[Mrtrix-discussion] tracks2prob, sample and resample doubts

[Luis Morís]

Hello list,

I'm trying to do a study with the streamlines produced by mrtrix.

My idea is to create an image similar to the one produced by
tracks2prob, but I have bumped into some problems.

I have created a function similar to tracks2prob into matlab. The idea
is really simple take the coordinates provided by streamtrack, and
load them into matlab (no problem here). Afterwards transform these
coordinates into voxel space, by using the transform matrix in the dwi
image, I round up the values and have the correct voxel coordinates.
But here I get a similar, but not identical, image as the one provided
by tracks2prob, I have checked the source code and it seems that this
process is not so straightforward, because some interpolation is made
along the way.

Could you explain the differences between my process and your process?
Is my idea correct or interpolation is a must fot the image to be
correct?

Is there a way of knowing which tracks are going through which voxel?
Or wich voxels do a track pass trough?

One of the parts of my study is related not only to the density of
tracks in a voxel, but with some scalars that will weight this density
or the contrary these scalar will be weighted by the track density.
i.e. Something similar to "The average pathlength map: a diffusion MRI
tractography-derived index for studying brain pathology. Pannek et
al." But for this purpose if I'm not wrong I need to know which tracks
pass through which voxel in order to calculate the average length of
the tracks that goes through a given voxel.

So that's why I ask if there's some way of getting this information
with mrtrix. I can do it with matlab, but as far as my method is not
similar to the one you use I want to make sure my approach is correct.


And a last question about sample and resample, if I have another image
for example Linear Anisotropy, I can use sample_tracks to obtain the
interpolated value of LA on each of the points of the track. And then
calculate for example the average LA in a given track. But as I've
read on the doc sample_tracks should be used with tracks produced by
resample_tracks to ensure even sampling. Why is that? Does not the
step size of 0.2 mm in streamtrack provide an even sampling? If I set
the -num (number of samples) parameter in resample_tracks to 100, All
tracks will have 100 points? Does that not do uneven sampling on
different size tracks? I mean do a 20 mm track have 100 samples, and a
200 mm track also 100 samples?


Thanks a lot in advance for your help, and sorry for the long post.

Best,

Luis Morís.