Hi Maia - It would still be probabilistic global tracrography, you'd just run it without anatomical priors since you don't have any prior knowledge of what areas your pathway goes through.
For each subject you'd need to define the two end ROIs of the pathway and (this is the trickier part) an initial guess for the pathway (a few control points on an imaginary curve that connects the two end ROIs). Is that easy to get for each subject? You could possibly pick the control points in MNI space and then map them back to each individual, if they align well.
You'd then run the dmri_paths command. Run it without any arguments and ignore anything other than the "basic inputs" section of the help. It's not particularly well-documented, since typically it's run through trac-all.
Hopefully this can get you started, let me know if you more questions.
a.y
On Mon, 17 Dec 2012, Maia Kipman wrote:
Good Morning, I would like to run deterministic global tracktography on 2 tracts for which tract tracing techniques in animals have established white matter connections. However, these tracts are not part of the 18 segmented in TRACULA. Because of crossing fibers, deterministic global tractography is more appropriate for the analysis I am running than local tracktography or probabilistic tractography. If I have run freesurfer segmentation for this cohort is there a mechanism I can use to run deterministic global tractography in the subjects native DWI space between two regions segmented by freesurfer?
Thanks!
Maia
Maia Kipman Study Coordinator Clinical Research Assistant Center for Depression, Anxiety and Stress Research McLean Hospital - Mail Stop #334 115 Mill Street Belmont, MA 02478 tel:(617)855-2239 mkipman@mclean.harvard.edu
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