Hi
You can use the --targetmasks and --os2t options :
probtrackx2 --seed=myseed.nii.gz --targetmasks=AsciiListOfTargets --os2t
[+ other options]
The list of targets can contain surface files, or volume files, or a
combination of both. If they are FreeSurfer label files, you will need to
first transform them into surface files using label2surf (see doc).
Cheers
Saad
> Dear FSL experts,
>
> I have gone through the manual, played a little with probatractx2 and
> glanced through some previous posts but could not find a simple solution
> to
> my problem. I have a seed mask that I got from a VBM study. I want to see
> how the detected structures connect to the rest of the brain. For that I
> generated target masks using Freesurfer aparc and aseg files. Now after
> running tractography I can view the tracts, but I want to quantify these
> in
> a connectivity matrix. The documentation says
>
> Matrix1 and Matrix2 store the number of samples (potentially modulated by
>> distance distance correction is used) between the rows (seed points) and
>> the columns of the matrix. Matrix3 stores the number of sample
>> streamlines
>> between each pair of points in a pair of target masks.
>
>
> I don't want any of those. Is there a direct way to do this? Or do I have
> to run for each seed-target pair and then concatenate the matrices?
>
> Thank you.
>
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