I would like to construct a connectivity matrix of the FreeSurfer Desikan-Killiany atlas using FSL’s Probtrackx2. I would like matrices showing ROI-to-ROI streamline count and mean path length. Using the example of this paper, I have gone ahead and set up a script that loops through each cortical ROI (
--seed) and computes streamlines to every other ROI (
--targetmasks). I was wondering if I could get some feedback on the current set up and see if there are specific options I should enable.
I am using all default options (i.e. streamline count of 5000, steplength of 0.5, curvature of 0.2, etc.), with
--pd flags enabled.
For outputs, I have specified
--s2tasrext, and '–network`.
For waypoint masks, I have specified the left and right cerebral white matter.
For exclusion masks, I am combining the DK-atlas CSF and ventricle parcellations into a single mask.
Does this seem like an efficient setup? Is there a recommended way to make running this more efficient? Thank you for any clarification you can provide!