Hi,
> On 4 Dec 2017, at 19:21, SUBSCRIBE FSL area51 <[log in to unmask]> wrote:
>
> I have a single seed to 7 targets. I am running probtrackx2 using the projection threshold option with a threshold of 1250. Now I get 7 seeds_to_target_proj_seg_thr files for each subject. My question is this:
>
> 1. Am I correct to interpret the values in these files as connection probability between each voxel in the seed to each of the targets?
In each seed voxel of the “seeds_to_*” files you have the raw streamline counts, i.e., how many streamlines connected that seed voxel to one of the target regions. If you want to get probability values, you should divide those numbers by the number in the waytotal file.
>
> 2. Is it logical to average the values over all voxels of the seed using the fslmaths -M option to get an "average connection probability" of the entire seed?
>
Once you’ve obtained probabilities using the previous step, you could get an average probability using something like:
fslstats seeds_to_target_1 -k seed_mask -m
> 3. Can the values be used to compare across subjects? That is, are they already normalized per subject using the waypoint number? That is, was this already incorporated into the projection threshold routine within probtrackx?
As I said before, you’ll need to do the normalisation by the waytotal yourself. You can then use those averaged probabilities to compare different subjects.
Hope this helps, cheers,
Matteo
|